PMFLib Wiki - User contributions [en]

Stm-trajectory

2026-06-19T11:50:39Z

Maintenance script:

{{DISPLAYTITLE:stm-trajectory}}
Navigation: [[Documentation]] / [[Utilities]] / [[stm-trajectory]]
----
<div style="text-align: center">stm-trajectory: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">stm-trajectory</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-trajectory</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">trjname</span> <span style="color: purple;">accuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It extracts a single snapshot from the STM trajectory.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">trjname</span><br/><div style="margin-left: 30px;">Name of file containing the STM trajectory. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file where a snapsphot (STM results) will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --snapshot NUMBER</span><br/><div style="margin-left: 30px;">Index of extracted snapshot (counted from 0).</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-server

2026-06-19T11:50:39Z

Maintenance script:

{{DISPLAYTITLE:stm-server}}
Navigation: [[Documentation]] / [[Utilities]] / [[stm-server]]
----
<div style="text-align: center">stm-server: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">stm-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It is the server for the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-admin

2026-06-19T11:50:38Z

Maintenance script:

{{DISPLAYTITLE:stm-admin}}
Navigation: [[Documentation]] / [[Utilities]] / [[stm-admin]]
----
<div style="text-align: center">stm-admin: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">stm-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">stm://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">stm://server[:port]/command</span><br/><div style="margin-left: 30px;">The server can be specified as either the DNS name, the IP address of the server, or the keyword 'serverkey' or 'key'. In the latter case, the server information is read from the server key file. The listening port number can be optionally provided. Finally, the command specifies an administrative task, which can be one of the following: <br />info = display information about registered clients<br />flush = save the accumulated STM path on the server side<br />get?file=output.path = retrieve the accumulated STM path and save it locally to the file 'output.path'<br />release?id=bead_id = unregister a client associated with the specified bead ID<br />terminate = terminate the server at the end of the STM cycle<br />shutdown = stop the server execution<br />errors = display errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Pmf-integrate

2026-06-19T11:50:38Z

Maintenance script:

{{DISPLAYTITLE:pmf-integrate}}
Navigation: [[Documentation]] / [[Utilities]] / [[pmf-integrate]]
----
<div style="text-align: center">pmf-integrate: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">pmf-integrate</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">pmf-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">ACCU</span> <span style="color: purple;">ENE</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program numerically integrates data from the PMF calculations. The integration is performed either by the reverse finite difference (RFD) method, radial basis functions (RBF), or Gaussian process (GPR).</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">ACCU</span><br/><div style="margin-left: 30px;">Name of the file containing the input PMF accumulator.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">ENE</span><br/><div style="margin-left: 30px;">Name of file where the resulting energy surface will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --realm NAME</span><br/><div style="margin-left: 30px;">Requested realm for the integration. The list of supported realms can be obtained by --listrealms.</div><span style="color:purple; margin-left: 30px;">(Default: dA/dx)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--listrealms</span><br/><div style="margin-left: 30px;">List supported realms.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Integration method. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (Gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--emethod NAME</span><br/><div style="margin-left: 30px;">Integration method for the energy cut-off. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (Gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide-and-conquer driver), svd2 (SVD - singular value decomposition, simple driver), qr (QR factorization), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: RFD(LU, default), RBF(QR, SVD, default), and GPR(LU, SVD, SVD2, LL, default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--rcond NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Rank condition for SVD. The selected value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 1000)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--skipfftest</span><br/><div style="margin-left: 30px;">Skip flood-fill test for discontinuous regions.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-q, --energylimit NUMBER</span><br/><div style="margin-left: 30px;">Integrate data only if the free energy is below NUMBER. This limit enforces two integration runs. A negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--rmnegene</span><br/><div style="margin-left: 30px;">Remove regions with negative free energy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--skiplastelimit</span><br/><div style="margin-left: 30px;">Skip energy limit filtering after the final integration.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--mfmaxzscore NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Reject mean forces whose prediction errors have a z-score above NUMBER. It is assumed that mean force errors have zero mean and follow a normal distribution. This limit is applied in each pass. A negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfnumofztests NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Repeat the z-score test for mean force errors NUMBER times.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: Factors influencing widths of RBFs or squared exponential kernels. The width is the distance between adjacent squared exponential functions, multiplied by these factors, in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-n, --sigman2 SPEC</span><br/><div style="margin-left: 30px;">GPR: Values of noise sigma squared for each CV, in the form SigmaN2(1)[xSigmaN2(2)x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 0.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file containing GPR hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-t, --rfac SPEC</span><br/><div style="margin-left: 30px;">RBF: Reduction factor for the number of RBFs. The number of RBFs in a given direction is the number of bins in that direction divided by this factor, in the form RFac1[xRFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-g, --overhang NUMBER</span><br/><div style="margin-left: 30px;">RBFs overhang to properly integrate areas near sampled edges. Ignored for periodic CVs.</div><span style="color:purple; margin-left: 30px;">(Default: 2)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--includeglued</span><br/><div style="margin-left: 30px;">RBF+GPR: Explicitly include glued regions. This option is set ON when --glueing > 0.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--glueing NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled bins in close vicinity to sampled ones.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--glueholes</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled regions inside the FES.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">RFD: Enable periodicity for collective variables that are periodic.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">RFD+RBF+GPR: Position of the global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination). If not set, the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate free energy errors.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noenergy</span><br/><div style="margin-left: 30px;">GPR: Skip calculation of energy and errors (can save time when only logML is required).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--saveaccu NAME</span><br/><div style="margin-left: 30px;">Save the final PMF accumulator to the file NAME.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">RBF+GPR: Name of file containing input and predicted mean forces.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print the free energy surface. Supported formats are: plain, gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall NAME</span><br/><div style="margin-left: 30px;">Print results for all bins, even if they are not properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled regions to the maximum energy from the sampled region, or to the value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used for unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print a header in the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1 = sampled, 0 = unsampled, -1 = glued) in the resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--oldrfd</span><br/><div style="margin-left: 30px;">RFD: Use the old RFD implementation.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">RFD: Number of points used in the differentiation scheme (three or four points are supported) in the RFD method.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default (= ardse).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">GPR: Use numerical differentiation of the kernel function (for testing only).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">GPR: Use the matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">GPR: Calculate logPL.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">GPR: Include zero-point energy at the position specified by --globalmin.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nofasterror</span><br/><div style="margin-left: 30px;">GPR: Do not use the faster algorithm for error calculation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--slevel VALUE</span><br/><div style="margin-left: 30px;">Sigma-level for the confidence interval.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--keepcvs SPEC</span><br/><div style="margin-left: 30px;">Which CVs should be kept during statistical reweighting of the FES. Flags are specified in the form CV1[xCV2x...] with F and T for skipped and kept CVs, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: T)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--reducedfes NAME</span><br/><div style="margin-left: 30px;">Name of file for FES reduced by statistical reweighting, containing only kept CVs.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Pmf-energy

2026-06-19T11:50:37Z

Maintenance script:

{{DISPLAYTITLE:pmf-energy}}
Navigation: [[Documentation]] / [[Utilities]] / [[pmf-energy]]
----
<div style="text-align: center">pmf-energy: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">pmf-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">pmf-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">ACCU</span> <span style="color: purple;">ENE</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program provides various types of energies from the PMF accumulator.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">ACCU</span><br/><div style="margin-left: 30px;">Name of the file containing the input PMF accumulator.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">ENE</span><br/><div style="margin-left: 30px;">Name of file where the resulting energy surface will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --realm NAME</span><br/><div style="margin-left: 30px;">Intended output. The list of supported realms can be obtained by --listrealms.</div><span style="color:purple; margin-left: 30px;">(Default: dU)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--listrealms</span><br/><div style="margin-left: 30px;">List supported realms.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Supported methods: raw (data taken directly from the accumulator) and gpr (Gaussian process filtered data).</div><span style="color:purple; margin-left: 30px;">(Default: raw)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --absolute</span><br/><div style="margin-left: 30px;">Absolute energy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate energy errors from the GPR model. RAW: Print energy errors from the PMF accumulator.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), ardmc32 (ARD Matern class 3/2), ardmc12 (ARD Matern class 1/2), default (=ardse).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fdkernel</span><br/><div style="margin-left: 30px;">Use the first derivatives of the GPR kernel (only for SmootherGPR).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">GPR: Calculate logPL.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: Variance of the reconstructed energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">GPR: Factors influencing widths of squared exponential kernels. The width is the distance between adjacent squared exponential functions multiplied by these factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-n, --sigman2 SPEC</span><br/><div style="margin-left: 30px;">Values of noise sigma squared for each CV in the form SigmaN2(1)[xSigmaN2(2)x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-5)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file containing the GPR hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--slevel VALUE</span><br/><div style="margin-left: 30px;">Sigma-level for the confidence interval.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file with input and predicted energy.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">GPR: Position of the global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination). If not set, the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify the integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled regions to the maximum energy from sampled regions or to the value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used for unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1 = sampled, 0 = unsampled, -1 = glued) in the resulting FES.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT for printing the energy surface. Supported formats: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print a header to the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins, even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT for printing values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT for printing results.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--lmethod NAME</span><br/><div style="margin-left: 30px;">GPR: Linear algebra method for LLS solution or matrix inversion. Supported algorithms: svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations: GPR(LU, SVD, SVD2, LL, default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--rcond NUMBER</span><br/><div style="margin-left: 30px;">GPR: Rank condition for SVD. The chosen value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mwa-server

2026-06-19T11:50:37Z

Maintenance script:

{{DISPLAYTITLE:mwa-server}}
Navigation: [[Documentation]] / [[Utilities]] / [[mwa-server]]
----
<div style="text-align: center">mwa-server: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">mwa-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mwa-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">mwa-server</span> is the server for the multiple walkers extension in PMFLib.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mwa-admin

2026-06-19T11:50:36Z

Maintenance script:

{{DISPLAYTITLE:mwa-admin}}
Navigation: [[Documentation]] / [[Utilities]] / [[mwa-admin]]
----
<div style="text-align: center">mwa-admin: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">mwa-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mwa-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">mwa://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">This utility controls the state and behavior of the server providing the multiple walkers extension for PMFLib.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">mwa://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated ABF data on the server side<br />get?file=NAME = get the accumulated ABF data and saves them locally to the NAME file (the default name is _mwaserver.rst)<br />shutdown = stop the server execution (use --force to skip protection by passphrase)<br />errors = print errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-f, --force</span><br/><div style="margin-left: 30px;">Skip protection of server shutdown by passphrase.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mtd-energy

2026-06-19T11:50:36Z

Maintenance script:

{{DISPLAYTITLE:mtd-energy}}
Navigation: [[Documentation]] / [[Utilities]] / [[mtd-energy]]
----
<div style="text-align: center">mtd-energy: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">mtd-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">mtd-energy</span> calculates the free energy surface estimate from the MTD accumulator file.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">Input file name containing the MTD accumulator or trajectory file with MTD accumulators or '-' to read data from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Output file name for the free energy surface or '-' to write data to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--floating</span><br/><div style="margin-left: 30px;">Keep FES floating.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --smooth NUMBER</span><br/><div style="margin-left: 30px;">Calculate average from specified number of MTD accumulators counted from the end of the trajectory file.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an energy offset.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Gpr-opthyprms

2026-06-19T11:50:35Z

Maintenance script:

{{DISPLAYTITLE:gpr-opthyprms}}
Navigation: [[Documentation]] / [[Utilities]] / [[gpr-opthyprms]]
----
<div style="text-align: center">gpr-opthyprms: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">gpr-opthyprms</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">gpr-opthyprms</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">ACCU</span> <span style="color: purple;">REALM</span> <span style="color: purple;">HYPRMS</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program finds optimal GPR hyperparameters, which maximize logarithm of marginal likelihood. The optimization is performed by the L-BFGS optimizer employing either analytical or numerical gradients of logML w.r.t. hyperparameters.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">ACCU</span><br/><div style="margin-left: 30px;">Name of the file containing the input PMF accumulator.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">REALM</span><br/><div style="margin-left: 30px;">Realm for GPR hyperparameter optimization. The list of supported realms can be obtained by --listrealms.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">HYPRMS</span><br/><div style="margin-left: 30px;">Name of the file containing the optimized hyperparameters.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--listrealms</span><br/><div style="margin-left: 30px;">List supported realms.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-t, --target NAME</span><br/><div style="margin-left: 30px;">Specify the optimized target, which can be either logml (log of marginal likelihood) or logpl (log of pseudo-likelihood from leave-one-out cross-validation, LOO-CV).</div><span style="color:purple; margin-left: 30px;">(Default: logml)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 1000)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for matrix inversion. Supported algorithms: default, svd (SVD – singular value decomposition, divide-and-conquer driver), svd2 (SVD – singular value decomposition, simple driver), lu (LU factorization), and ll (LL – Cholesky factorization).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">Rank condition for SVD. The chosen value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 SPEC</span><br/><div style="margin-left: 30px;">Variance of the reconstructed free-energy surface (signal variance) in the form SigmaF2(1)[xSigmaF2(2)[x...]]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 15.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--minsigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">Minimum value of SigmaF2.</div><span style="color:purple; margin-left: 30px;">(Default: 0.1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --covar SPEC</span><br/><div style="margin-left: 30px;">Covariances between GPR tasks in the form CoVar1[xCoVar2[x...]]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 0.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mincovar NUMBER</span><br/><div style="margin-left: 30px;">Minimum value of CoVar.</div><span style="color:purple; margin-left: 30px;">(Default: -1000)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">Characteristic scale of collective variables in the form WFac1[xWFac2[x...]]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--minwfac NUMBER</span><br/><div style="margin-left: 30px;">Minimum value of WFac.</div><span style="color:purple; margin-left: 30px;">(Default: 0.1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-n, --sigman2 SPEC</span><br/><div style="margin-left: 30px;">Noise variances (σ²) for each CV in the form SigmaN2(1)[xSigmaN2(2)[x...]]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-5)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--minsigman2 NUMBER</span><br/><div style="margin-left: 30px;">Minimum value of SigmaN2.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablesigmaf2 SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of SigmaF2 hyperparameters. Flags are specified in the form SigmaF2(1)Enabled[xSigmaF2(2)Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablecovar SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of CoVar hyperparameters. Flags are specified in the form CoVar1Enabled[xCoVar2Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablewfac SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of WFac hyperparameters. Flags are specified in the form WFac1Enabled[xWFac2Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablesigman2 SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of SigmaN2 hyperparameters. Flags are specified in the form SigmaN2(1)Enabled[xSigmaN2(2)Enabled[x...]] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--numeric</span><br/><div style="margin-left: 30px;">Use numerical gradients.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noptsteps NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of optimization steps.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nresets NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of resets due to insufficient optimization progress.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--termeps NUMBER</span><br/><div style="margin-left: 30px;">Termination criterion for the L-BFGS optimizer (see L-BFGS code).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-05)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--termval NUMBER</span><br/><div style="margin-left: 30px;">Termination criterion for the L-BFGS optimizer. Minimum change of the optimized property.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nlbfgscorr NUMBER</span><br/><div style="margin-left: 30px;">Number of corrections used in an L-BFGS update.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--test</span><br/><div style="margin-left: 30px;">Compare analytical and numerical gradients for input hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--cd5</span><br/><div style="margin-left: 30px;">Use the 5-point stencil for numerical differentiation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">Name of the file containing the GPR hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--stat</span><br/><div style="margin-left: 30px;">Calculate detailed GPR statistics using the optimized hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--sptype</span><br/><div style="margin-left: 30px;">Determine the type of stationary point.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matérn class 5/2), default (=ardse).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fdkernel</span><br/><div style="margin-left: 30px;">Use the first derivatives of the GPR kernel (only for SmootherGPR).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">Use the matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">Calculate logPL for --stat if --target is not logpl.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">Position of the global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination). If not set, the position is determined automatically.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Aus-integrate

2026-06-19T11:50:35Z

Maintenance script:

{{DISPLAYTITLE:aus-integrate}}
Navigation: [[Documentation]] / [[Utilities]] / [[aus-integrate]]
----
<div style="text-align: center">aus-integrate: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">aus-integrate</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">aus-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">ACCU</span> <span style="color: purple;">FEN</span> <span style="color: purple;">INT</span> <span style="color: purple;">TDS</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program numerically integrates data from the ABF calculation.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">ACCU</span><br/><div style="margin-left: 30px;">Name of the file containing the input ABF accumulator.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">FEN</span><br/><div style="margin-left: 30px;">Name of the file containing the output free energy surface [dA(x)].</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">INT</span><br/><div style="margin-left: 30px;">Name of the file containing the output internal energy surface [dU(x)].</div>
|- style="vertical-align: top;"
| <span style="color: purple;">TDS</span><br/><div style="margin-left: 30px;">Name of the file containing the output entropic energy surface [-TdS(x)].</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--constraints</span><br/><div style="margin-left: 30px;">Impose constraints: dA(x)/dx - dU(x)/dx - (-TdS(x)/dx) = 0.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-r, --realm NAME</span><br/><div style="margin-left: 30px;">Requested realm for data processing. The list of supported realms can be obtained by --listrealms.</div><span style="color:purple; margin-left: 30px;">(Default: AUS)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--listrealms</span><br/><div style="margin-left: 30px;">List supported realms.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms: default, svd (SVD - divide and conquer), svd2 (SVD - simple), qr (QR factorization), lu (LU factorization), ll (Cholesky factorization). Possible combinations: GPR(LU, SVD, SVD2, LL, default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--rcond NUMBER</span><br/><div style="margin-left: 30px;">Rank condition for SVD. The chosen value must be carefully tested. Calculation at machine precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 1000)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --sigmaf2 SPEC</span><br/><div style="margin-left: 30px;">Signal variances for each realm in the form SigmaF2(1)[xSigmaF2(2)x...]. The last value pads the rest. There are three realms.</div><span style="color:purple; margin-left: 30px;">(Default: 15.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-c, --covar SPEC</span><br/><div style="margin-left: 30px;">Signal covariances for each realm in the form CoVar(1)[xCoVar(2)x...]. The last value pads the rest. There are three realms.</div><span style="color:purple; margin-left: 30px;">(Default: 0.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">Factors influencing widths of RBFs or squared exponential kernels. The width is the distance between adjacent functions multiplied by these factors, in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-n, --sigman2 SPEC</span><br/><div style="margin-left: 30px;">Noise variances (sigma squared) for each CV in the form SigmaN2(1)[xSigmaN2(2)x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 0.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">Name of the file containing GPR hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">Position of the global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination). If not set, the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify the integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">Estimate free energy errors.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noenergy</span><br/><div style="margin-left: 30px;">Skip calculation of energy and errors (saves time when only logML is required).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--balres</span><br/><div style="margin-left: 30px;">Balance residual errors between dG, dH, and -TdS.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">Name of the file with input and predicted mean forces.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--residuals NAME</span><br/><div style="margin-left: 30px;">Name of the file with residuals values.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output format for printing the free energy surface. Supported formats: plain, gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled regions to the maximum energy from sampled regions or to the value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">Energy value used for unsampled regions if set.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print a header in the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) in the resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output format used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output format used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default (=ardse).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdkernel</span><br/><div style="margin-left: 30px;">Use the first derivatives of the GPR kernel (only for SmootherGPR).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">Use numerical differentiation of the kernel function (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">Calculate logPL.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nofasterror</span><br/><div style="margin-left: 30px;">Do not use the faster algorithm for error calculation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--slevel VALUE</span><br/><div style="margin-left: 30px;">Sigma level for confidence intervals.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help message and exit.</div>
|}

Accu-trajectory

2026-06-19T11:50:34Z

Maintenance script:

{{DISPLAYTITLE:accu-trajectory}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-trajectory]]
----
<div style="text-align: center">accu-trajectory: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">accu-trajectory</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-trajectory</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">trjname</span> <span style="color: purple;">outname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-trajectory</span> extracts a single snapshot from the trajectory of PMF accumulators.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">trjname</span><br/><div style="margin-left: 30px;">Name of file containing the PMF accumulator trajectory. If the name is '-' then the trajectory is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">outname</span><br/><div style="margin-left: 30px;">Name of file where a snapsphot (PMF accumulator) will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --snapshot NUMBER</span><br/><div style="margin-left: 30px;">Index of extracted snapshot (counted from 1).</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Accu-info

2026-06-19T11:50:34Z

Maintenance script:

{{DISPLAYTITLE:accu-info}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-info]]
----
<div style="text-align: center">accu-info: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">accu-info</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-info</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname action [section]</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-info</span> prints info about the PMF accumulator file and extracts data from it.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname</span></span> Input name of PMF accumulator or '-' to read it from the standard input.<br /><span style="color: darkcyan;"><span style="font-style: bold;">action</span></span> Requested action:<br /><span></span> ** <span style="font-style: bold;">info</span> - print summary about the accumulator<br /><span></span> ** <span style="font-style: bold;">list-sections</span> - print available sections<br /><span></span> ** <span style="font-style: bold;">get-section</span> - get data from the section<br /><span></span> ** <span style="font-style: bold;">get-derivative</span> - get derivative for given realm<br /><span></span> ** <span style="font-style: bold;">get-energy</span> - get energy for given realm<br /><span></span> ** <span style="font-style: bold;">get-mean</span> - get sample mean, variance, and mean error<br /><span></span> ** <span style="font-style: bold;">get-tseries</span> - get time series<br /><span></span> ** <span style="font-style: bold;">nsamples</span> - print number of samples in bins</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Report only bins containing more samples than the specified NUMBER.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-i, --item CV</span><br/><div style="margin-left: 30px;">Select the collective variable (CV) for data output.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">Disable printing of delimiters between records.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print the header in the output.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Format string for printing values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Format string for printing values of section data.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase the verbosity of the output.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Display version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help message and exit.</div>
|}

Accu-combine

2026-06-19T11:50:33Z

Maintenance script:

{{DISPLAYTITLE:accu-combine}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-combine]]
----
<div style="text-align: center">accu-combine: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">accu-combine</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-combine</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname1 [accuname2 [..]] outaccuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-combine</span> combines more PMF accumulators into one. All PMF accumulators have to be of the same dimensions and contain data from the same PMF method.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname1</span></span> File name of the PMF accumulator.<br /><span style="color: darkcyan;"><span style="font-style: bold;">outaccuname</span></span> File name of the resulting PMF accumulator.</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--linear</span><br/><div style="margin-left: 30px;">Combine PMF accumulators by step-by-step algorithm.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--common</span><br/><div style="margin-left: 30px;">Combine only common data sections.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abp-energy

2026-06-19T11:50:32Z

Maintenance script:

{{DISPLAYTITLE:abp-energy}}
Navigation: [[Documentation]] / [[Utilities]] / [[abp-energy]]
----
<div style="text-align: center">abp-energy: version 6.1090.a7cf688 (2026-06-18 21:15)</div>'''Name'''

<span style="margin-left: 15px;">abp-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abp-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It calculate the free energy surface estimate from the metadynamics restart file.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">Name of file containing the ABP restart file. If the name is '-' then the file is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --mode NAME</span><br/><div style="margin-left: 30px;">Energy calculation mode: mollified (use raw mollified FES), rl (Lucy-Richardson deconvolution)</div><span style="color:purple; margin-left: 30px;">(Default: rl)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--rliter NUMBER</span><br/><div style="margin-left: 30px;">Number of Lucy-Richardson deconvolution iteration.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--floating</span><br/><div style="margin-left: 30px;">Keep FES floating.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-server

2021-07-28T12:45:44Z

Maintenance script:

{{DISPLAYTITLE:stm-server}}
Navigation: [[Documentation]] / [[Utilities]] / [[stm-server]]
----
<div style="text-align: center">stm-server: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">stm-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It is the server for the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-admin

2021-07-28T12:45:44Z

Maintenance script:

{{DISPLAYTITLE:stm-admin}}
Navigation: [[Documentation]] / [[Utilities]] / [[stm-admin]]
----
<div style="text-align: center">stm-admin: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">stm-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">stm://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">stm://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated STM path on the server side<br />get?file=output.path = get the accumulated STM path and save it locally to the file output.path <br />release?id=bead_id = unregister a client bound to the bead<br />terminate = terminate server at the end of STM cycle<br />shutdown = stop server execution<br />errors = prints errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Pmf-integrate

2021-07-28T12:45:43Z

Maintenance script:

{{DISPLAYTITLE:pmf-integrate}}
Navigation: [[Documentation]] / [[Utilities]] / [[pmf-integrate]]
----
<div style="text-align: center">pmf-integrate: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">pmf-integrate</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">pmf-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname fename [fullfename]</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program numerically integrates data from the PMF calculations. The integration is performed either by the reverse finite difference (RFD) method, radial basis functions (RBF), or Gaussian process (GPR).</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname</span></span> Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fename</span></span> Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fullfename</span></span> Optional name of file with free energy surface containing all regions (sampled and unsampled).</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --realm NAME</span><br/><div style="margin-left: 30px;">Intended output from the integration:<br />** dG - free energy (default)<br />** -TdS - entropy contribution to the free energy<br />** dG_p - free energy (potential part) - ABF<br />** dG_k - free energy (kinetic part) - ABF<br />** -TdS_PP - entropy contribution to the free energy, cov(dH_p/dx,Epot) - ABF<br />** -TdS_PK - entropy contribution to the free energy, cov(dH_p/dx,Ekin) - ABF<br />** -TdS_PR - entropy contribution to the free energy, cov(dH_p/dx,Erst) - ABF<br />** -TdS_KP - entropy contribution to the free energy, cov(dH_k/dx,Epot) - ABF<br />** -TdS_KK - entropy contribution to the free energy, cov(dH_k/dx,Ekin) - ABF<br />** -TdS_KR - entropy contribution to the free energy, cov(dH_k/dx,Erst) - ABF<br />** -TdS_HP - entropy contribution to the free energy, cov(dH/dx,Epot) - CST<br />** -TdS_HK - entropy contribution to the free energy, cov(dH/dx,Ekin) - CST<br />** -TdS_HR - entropy contribution to the free energy, cov(dH/dx,Erst) - CST</div><span style="color:purple; margin-left: 30px;">(Default: dG)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Integration method. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--emethod NAME</span><br/><div style="margin-left: 30px;">Integration method for energy cut-off. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), qr (QR factorization), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: RFD(LU,default), RBF(QR,SVD,default), and GPR(LU,SVD,SVD2,LL,default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--rcond NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--skipfftest</span><br/><div style="margin-left: 30px;">Skip flood fill test for discontinuous regions.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-q, --energylimit NUMBER</span><br/><div style="margin-left: 30px;">Integrate data only if the free energy is below NUMBER. This limit enforces two integration runs. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--rmnegene</span><br/><div style="margin-left: 30px;">Remove regions with negative free energy.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--skiplastelimit</span><br/><div style="margin-left: 30px;">Skip energy limit filter after final integration.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfmaxzscore NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Reject mean forces whose errors in prediction have z-score above NUMBER. In the test, it is assumend that mean force errors have zero mean and they follow normal distribution. This limit is aplied in the each pass. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--mfnumofztests NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Repeat z-score test for mean force errrors NUMBER times.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-c, --ncorr NUMBER</span><br/><div style="margin-left: 30px;">GPR: Number of statistically correlated samples.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: Factors influencing widths of RBFs or square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file with GPR hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --rfac SPEC</span><br/><div style="margin-left: 30px;">RBF: Reduction factor for number of RBFs. Number of RBFs in given direction is number of bins in that direction divided by this factor in the form RFac1[xRFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-g, --overhang NUMBER</span><br/><div style="margin-left: 30px;">RBFs overhang to properly integrate areas near sampled edges. Ignored for periodic CVs.</div><span style="color:purple; margin-left: 30px;">(Default: 2)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includeglued</span><br/><div style="margin-left: 30px;">RBF+GPR: Explicitly include glued regions. This options is set ON when --glueing > 0.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--glueing NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled bins in close vicinity to sampled ones.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--glueholes</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled regions inside the FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">RFD: Switch on periodicity for collective variables that are periodic.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--userealglbmin</span><br/><div style="margin-left: 30px;">RBF+GPR: ignore --globalmin in the final integration step</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate free energy errors.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noenergy</span><br/><div style="margin-left: 30px;">GPR: Skip calculation of energy and errors (it can save some time when only logML is required).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--saveabf NAME</span><br/><div style="margin-left: 30px;">Save the final ABF accumulator into the file with NAME.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">RBF+GPR: name of file with input and predicted mean forces.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print the free energy surface. Supported formats are: plain, and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--oldrfd</span><br/><div style="margin-left: 30px;">RFD: Use old RFD implementation.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">RFD: Determine number of points employed in differenciation scheme (three or four is upported) in RFD method.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">GPR: Use numerical differentiation of kernel function (for testing only).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">GPR: Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">GPR: Calculate logPL.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">GPR: Include zero-point energy at position specified by --globalmin.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nofasterror</span><br/><div style="margin-left: 30px;">GPR: Do not use faster algorithm for error calculation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--slevel VALUE</span><br/><div style="margin-left: 30px;">Sigma-level for confidence interval.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--keepcvs SPEC</span><br/><div style="margin-left: 30px;">Which CVs should be kept during statistical reweighting of FES. Flags are specified in the form CV1[xCV2x...] with F and T for skip and kept CV, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: T)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--reducedfes NAME</span><br/><div style="margin-left: 30px;">Name of file for FES reduced by statistical reweighting containing only kept CVs.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Pmf-enthalpy

2021-07-28T12:45:42Z

Maintenance script:

{{DISPLAYTITLE:pmf-enthalpy}}
Navigation: [[Documentation]] / [[Utilities]] / [[pmf-enthalpy]]
----
<div style="text-align: center">pmf-enthalpy: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">pmf-enthalpy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">pmf-enthalpy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">enthalpy</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program provides enthalpy from the PMF accumulator.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the PMF accumulator. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">enthalpy</span><br/><div style="margin-left: 30px;">Name of file where results will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --realm NAME</span><br/><div style="margin-left: 30px;">Intended output:<br />** - enthalpy as the ensemble average of the potential energy (default)<br />** - the ensemble average of the kinetic energy (this should be a constant for simulations at a constant temperature)<br />** - the ensemble average of the PMFLib restrain energy<br />** - enthalpy as the ensemble average of the total energy</div><span style="color:purple; margin-left: 30px;">(Default: <Epot>)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Supported methods are: raw (data taken directly from accumulator) and gpr (gaussian process filtered data).</div><span style="color:purple; margin-left: 30px;">(Default: raw)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-a, --absolute</span><br/><div style="margin-left: 30px;">absolute enthalpy.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate enthalpy errors from the GPR model. RAW: Print enthalpy errors from the PMF accumulator.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: Variance of the reconstructed enthalpy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-c, --ncorr VALUE</span><br/><div style="margin-left: 30px;">Number of statistically correlated samples.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">GPR: Factors influencing widths of square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file with the GPR hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--slevel VALUE</span><br/><div style="margin-left: 30px;">Sigma-level for confidence interval.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">GPR: position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print the enthalpy surface. Supported formats are: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print results.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: GPR(LU,SVD,SVD2,LL,default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--rcond NUMBER</span><br/><div style="margin-left: 30px;">GPR: Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mwa-server

2021-07-28T12:45:41Z

Maintenance script:

{{DISPLAYTITLE:mwa-server}}
Navigation: [[Documentation]] / [[Utilities]] / [[mwa-server]]
----
<div style="text-align: center">mwa-server: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">mwa-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mwa-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">mwa-server</span> is the server for the multiple walkers extension in PMFLib.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mwa-admin

2021-07-28T12:45:41Z

Maintenance script:

{{DISPLAYTITLE:mwa-admin}}
Navigation: [[Documentation]] / [[Utilities]] / [[mwa-admin]]
----
<div style="text-align: center">mwa-admin: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">mwa-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mwa-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">mwa://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">This utility controls the state and behavior of the server providing the multiple walkers extension for PMFLib.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">mwa://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated ABF data on the server side<br />get?file=NAME = get the accumulated ABF data and saves them locally to the NAME file (the default name is _abfserver.rst)<br />shutdown = stop the server execution (use --force to skip protection by passphrase)<br />errors = print errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-f, --force</span><br/><div style="margin-left: 30px;">Skip protection of server shutdown by passphrase.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mtd-energy

2021-07-28T12:45:40Z

Maintenance script:

{{DISPLAYTITLE:mtd-energy}}
Navigation: [[Documentation]] / [[Utilities]] / [[mtd-energy]]
----
<div style="text-align: center">mtd-energy: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">mtd-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">mtd-energy</span> calculates the free energy surface estimate from the MTD accumulator file.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">Input file name containing the MTD accumulator or trajectory file with MTD accumulators or '-' to read data from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Output file name for the free energy surface or '-' to write data to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--floating</span><br/><div style="margin-left: 30px;">Keep FES floating.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --smooth NUMBER</span><br/><div style="margin-left: 30px;">Calculate average from specified number of MTD accumulators counted from the end of the trajectory file.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Gpr-opthyprms

2021-07-28T12:45:39Z

Maintenance script:

{{DISPLAYTITLE:gpr-opthyprms}}
Navigation: [[Documentation]] / [[Utilities]] / [[gpr-opthyprms]]
----
<div style="text-align: center">gpr-opthyprms: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">gpr-opthyprms</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">gpr-opthyprms</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname1 realm1 [accuname2 realm2 [..]] hyprmsname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program finds optimal GPR hyperparameters, which maximize logarithm of marginal likelihood. The optimization is performed by the L-BFGS optimizer employing either analytical or numerical gradients of logML w.r.t. hyperparameters.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname1</span></span> Name of file containing the PMF accumulator.<br /><span style="color: darkcyan;"><span style="font-style: bold;">realm1</span></span> Realm of interest.<br /><span style="color: darkcyan;"><span style="font-style: bold;">hyprmsname</span></span> Name of file where the optimized GPR hyperparameters are saved. If the name is '-' then the output will be written to the standard output.</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --target NAME</span><br/><div style="margin-left: 30px;">Specify optimized targed, which can be either logml (log of marginal likelihood) or logpl (log of pseudo-likelihood from leave-one-out cross-validation (LOO-CV)).</div><span style="color:purple; margin-left: 30px;">(Default: logml)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), and ll (LL - Cholesky factorization).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-c, --ncorr NUMBER</span><br/><div style="margin-left: 30px;">Number of statistically correlated samples.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">Factors influencing widths of RBFs or square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablesigmaf2</span><br/><div style="margin-left: 30px;">Enable optimization of SigmaF2 hyperparameter.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablencorr</span><br/><div style="margin-left: 30px;">Enable optimization of NCorr hyperparameter.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablewfac SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of Wfac hyperparamters. Flags are specified in the form WFac1Enabled[xWFac2Enabledx...] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--numeric</span><br/><div style="margin-left: 30px;">Use numeric gradients.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noptsteps NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of optimization steps.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nresets NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of resets due to insufficient optimization progress.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--termeps NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer (see L-BFGS code).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-05)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--termval NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer. Minimum change of optimized property.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nlbfgscorr NUMBER</span><br/><div style="margin-left: 30px;">Number of corrections used in an L-BFGS update.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--test</span><br/><div style="margin-left: 30px;">Compare analytical and numerical gradient for input hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--cd5</span><br/><div style="margin-left: 30px;">Use 5-point stencil for numerical differentiation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">Name of file with GPR hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--stat</span><br/><div style="margin-left: 30px;">Calculate detailed GPR status employing found hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--sptype</span><br/><div style="margin-left: 30px;">Determine type of stationary point.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">Calculate logPL for --stat if --target is not logpl.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Accu-trajectory

2021-07-28T12:45:38Z

Maintenance script:

{{DISPLAYTITLE:accu-trajectory}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-trajectory]]
----
<div style="text-align: center">accu-trajectory: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">accu-trajectory</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-trajectory</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">trjname</span> <span style="color: purple;">outname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-trajectory</span> extracts a single snapshot from the trajectory of PMF accumulators.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">trjname</span><br/><div style="margin-left: 30px;">Name of file containing the PMF accumulator trajectory. If the name is '-' then the trajectory is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">outname</span><br/><div style="margin-left: 30px;">Name of file where a snapsphot (PMF accumulator) will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --snapshot NUMBER</span><br/><div style="margin-left: 30px;">Index of extracted snapshot (counted from 1).</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Accu-info

2021-07-28T12:45:37Z

Maintenance script:

{{DISPLAYTITLE:accu-info}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-info]]
----
<div style="text-align: center">accu-info: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">accu-info</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-info</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname action [section]</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-info</span> prints info about the PMF accumulator file and extracts data from it.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname</span></span> Input name of PMF accumulator or '-' to read it from the standard input.<br /><span style="color: darkcyan;"><span style="font-style: bold;">action</span></span> Requested action:<br /><span></span> ** <span style="font-style: bold;">info</span> - print summary about the accumulator<br /><span></span> ** <span style="font-style: bold;">list-sections</span> - print available sections<br /><span></span> ** <span style="font-style: bold;">get-section</span> - get data from the section<br /><span></span> ** <span style="font-style: bold;">nsamples</span> - print number of samples in bins<br /><span></span> ** <span style="font-style: bold;">micf</span> - print mean ICF forces (only the ABF simulations)</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER will be reported.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-i, --item CV</span><br/><div style="margin-left: 30px;">Select CV for data printing.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">Do not print delimiters between records.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">FORMAT for printing values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">FORMAT for printing values of section data.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Accu-combine

2021-07-28T12:45:37Z

Maintenance script:

{{DISPLAYTITLE:accu-combine}}
Navigation: [[Documentation]] / [[Utilities]] / [[accu-combine]]
----
<div style="text-align: center">accu-combine: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">accu-combine</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">accu-combine</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname1 [accuname2 [..]] outaccuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">accu-combine</span> combines more PMF accumulators into one. All PMF accumulators have to be of the same dimensions and contain data from the same PMF method.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname1</span></span> File name of the PMF accumulator.<br /><span style="color: darkcyan;"><span style="font-style: bold;">outaccuname</span></span> File name of the resulting PMF accumulator.</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abp-energy

2021-07-28T12:45:35Z

Maintenance script:

{{DISPLAYTITLE:abp-energy}}
Navigation: [[Documentation]] / [[Utilities]] / [[abp-energy]]
----
<div style="text-align: center">abp-energy: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''

<span style="margin-left: 15px;">abp-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abp-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It calculate the free energy surface estimate from the metadynamics restart file.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">Name of file containing the ABP restart file. If the name is '-' then the file is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --mode NAME</span><br/><div style="margin-left: 30px;">Energy calculation mode: mollified (use raw mollified FES), rl (Lucy-Richardson deconvolution)</div><span style="color:purple; margin-left: 30px;">(Default: rl)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--rliter NUMBER</span><br/><div style="margin-left: 30px;">Number of Lucy-Richardson deconvolution iteration.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--floating</span><br/><div style="margin-left: 30px;">Keep FES floating.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain and gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-trajectory

2020-03-06T16:10:58Z

Maintenance script:

{{DISPLAYTITLE:stm-trajectory}}
Navigation: [[Documentation]] / [[Methods]] / [[String Method]] / [[STM:Utilities]] / [[stm-trajectory]]
----
{{STMUtils}}
<div style="text-align: center">stm-trajectory: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">stm-trajectory</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-trajectory</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">trjname</span> <span style="color: purple;">accuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It extracts a single snapshot from the STM trajectory.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">trjname</span><br/><div style="margin-left: 30px;">Name of file containing the STM trajectory. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file where a snapsphot (STM results) will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --snapshot NUMBER</span><br/><div style="margin-left: 30px;">Index of extracted snapshot (counted from 0).</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-server

2020-03-06T16:10:58Z

Maintenance script:

{{DISPLAYTITLE:stm-server}}
Navigation: [[Documentation]] / [[Methods]] / [[String Method]] / [[STM:Utilities]] / [[stm-server]]
----
{{STMUtils}}
<div style="text-align: center">stm-server: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">stm-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It is the server for the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Stm-admin

2020-03-06T16:10:57Z

Maintenance script:

{{DISPLAYTITLE:stm-admin}}
Navigation: [[Documentation]] / [[Methods]] / [[String Method]] / [[STM:Utilities]] / [[stm-admin]]
----
{{STMUtils}}
<div style="text-align: center">stm-admin: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">stm-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">stm-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">stm://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the string method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">stm://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated STM path on the server side<br />get?file=output.path = get the accumulated STM path and save it locally to the file output.path <br />release?id=bead_id = unregister a client bound to the bead<br />terminate = terminate server at the end of STM cycle<br />shutdown = stop server execution<br />errors = prints errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Rst-samples

2020-03-06T16:06:42Z

Maintenance script:

{{DISPLAYTITLE:rst-samples}}
Navigation: [[Documentation]] / [[Methods]] / [[Restrained Dynamics]] / [[RST:Utilities]] / [[rst-samples]]
----
{{RSTUtils}}
<div style="text-align: center">rst-samples: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">rst-samples</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">rst-samples</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">sname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It prints the number of samples accumulated during RST calculation.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">File name of the RST histogram file. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">sname</span><br/><div style="margin-left: 30px;">Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">only bins with the number of samples grater than or equal to LIMIT will be printed</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">do not print delimiters between records</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of coordinate values</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">output FORMAT of samples</div><span style="color:purple; margin-left: 30px;">(Default: %d)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
|}

Mtd-server

2020-03-06T16:01:15Z

Maintenance script:

{{DISPLAYTITLE:mtd-server}}
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-server]]
----
{{MTDUtils}}
<div style="text-align: center">mtd-server: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">mtd-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mtd-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It is the server for the multiple walkers extension of the metadynamics method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mtd-energy

2020-03-06T16:01:14Z

Maintenance script:

{{DISPLAYTITLE:mtd-energy}}
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]]
----
{{MTDUtils}}
<div style="text-align: center">mtd-energy: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">mtd-energy</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It calculate the free energy surface estimate from the metadynamics restart file.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">input</span><br/><div style="margin-left: 30px;">Name of file containing the metadynamics restart file. If the name is '-' then the file is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --time NUMBER</span><br/><div style="margin-left: 30px;">Specifies metadynamics time that will be used for the energy calculation.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--offset REAL</span><br/><div style="margin-left: 30px;">Determine position of global minima.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--smooth NUMBER</span><br/><div style="margin-left: 30px;">Calculate the energy surface average from time interval SMOOTH to TIME.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--sd</span><br/><div style="margin-left: 30px;">Print the standard deviation of the free energy when the smoothing is enabled.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fs FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of standard deviations.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7le)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Mtd-admin

2020-03-06T16:01:13Z

Maintenance script:

{{DISPLAYTITLE:mtd-admin}}
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-admin]]
----
{{MTDUtils}}
<div style="text-align: center">mtd-admin: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">mtd-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">mtd-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">mtd://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the multiple walkers extension of the metadynamics method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">mtd://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated MTD data on the server side<br />get?file=NAME = get the accumulated MTD data and saves them locally to the file with NAME<br />shutdown = stop the server execution<br />errors = print errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-optgprhyprms

2020-03-06T15:52:33Z

Maintenance script:

{{DISPLAYTITLE:abf-optgprhyprms}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-optgprhyprms]]
----
{{ABFUtils}}
<div style="text-align: center">abf-optgprhyprms: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-optgprhyprms</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-optgprhyprms</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname1 [accuname2 [..]] hyprmsname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">abf-optgprhyprms finds optimal GPR hyperparameters, which maximize logarithm of marginal likelihood. The optimization is performed by the L-BFGS optimizer employing either analytical or numerical gradients of logML w.r.t. hyperparameters.</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname1</span></span> Name of file containing the ABF accumulator.<br /><span style="color: darkcyan;"><span style="font-style: bold;">hyprmsname</span></span> Name of file where the optimized GPR hyperparameters are saved. If the name is '-' then the output will be written to the standard output.</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --target NAME</span><br/><div style="margin-left: 30px;">Specify optimized targed, which can be either logml (log of marginal likelihood) or logpl (log of pseudo-likelihood from leave-one-out cross-validation (LOO-CV)).</div><span style="color:purple; margin-left: 30px;">(Default: logml)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), and ll (LL - Cholesky factorization).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-c, --ncorr SPEC</span><br/><div style="margin-left: 30px;">GPR: Number of statistically correlated samples in the form NCorr1[xNCorr2x...]. The last value pads the rest. Split ncorr mode is enabled by the --splitncorr option.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--splitncorr</span><br/><div style="margin-left: 30px;">Use indepenedent ncorr for each CV.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">Factors influencing widths of RBFs or square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablesigmaf2</span><br/><div style="margin-left: 30px;">Enable optimization of SigmaF2 hyperparameter.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablencorr SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of NCorr hyperparameter. Flags are specified in the form Ncorr1Enabled[xNcorr2Enabledx...] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablewfac SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of Wfac hyperparamters. Flags are specified in the form WFac1Enabled[xWFac2Enabledx...] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--numeric</span><br/><div style="margin-left: 30px;">Use numeric gradients.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--noptsteps NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of optimization steps.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nresets NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of resets due to insufficient optimization progress.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--termeps NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer (see L-BFGS code).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-05)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--termval NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer. Minimum change of optimized property.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nlbfgscorr NUMBER</span><br/><div style="margin-left: 30px;">Number of corrections used in an L-BFGS update.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--test</span><br/><div style="margin-left: 30px;">Compare analytical and numerical gradient for input hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--cd5</span><br/><div style="margin-left: 30px;">Use 5-point stencil for numerical differentiation.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">Name of file with GPR hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--stat</span><br/><div style="margin-left: 30px;">Calculate detailed GPR status employing found hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--sptype</span><br/><div style="margin-left: 30px;">Determine type of stationary point.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">Use numerical differentiation of kernel function (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">Calculate logPL for --stat if --target is not logpl.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">Include zero-point energy at position specified by --globalmin.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-trajectory

2020-03-06T15:49:11Z

Maintenance script:

{{DISPLAYTITLE:abf-trajectory}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-trajectory]]
----
{{ABFUtils}}
<div style="text-align: center">abf-trajectory: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-trajectory</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-trajectory</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">trjname</span> <span style="color: purple;">accuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It extracts a single snapshot from the ABF accumulator trajectory.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">trjname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator trajectory. If the name is '-' then the trajectory is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file where a snapsphot (ABF accumulator) will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --snapshot NUMBER</span><br/><div style="margin-left: 30px;">Index of extracted snapshot (counted from 1).</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-server

2020-03-06T15:49:10Z

Maintenance script:

{{DISPLAYTITLE:abf-server}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-server]]
----
{{ABFUtils}}
<div style="text-align: center">abf-server: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-server</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-server</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">control</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It is the server for the multiple walkers extension of the ABF method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">control</span><br/><div style="margin-left: 30px;">Name of file containing the server configuration. If the name is '-' then the configuration is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-samples

2020-03-06T15:49:09Z

Maintenance script:

{{DISPLAYTITLE:abf-samples}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-samples]]
----
{{ABFUtils}}
<div style="text-align: center">abf-samples: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-samples</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-samples</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">sname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It prints number of samples accumulated during the ABF calculation.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">sname</span><br/><div style="margin-left: 30px;">Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">Do not print delimiters between records.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print samples.</div><span style="color:purple; margin-left: 30px;">(Default: %d)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-mask

2020-03-06T15:20:32Z

Maintenance script:

{{DISPLAYTITLE:abf-mask}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-mask]]
----
{{ABFUtils}}
<div style="text-align: center">abf-mask: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-mask</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-mask</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">mask</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It create the ABF accumulator mask according to user specified criteria.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">mask</span><br/><div style="margin-left: 30px;">Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --maxene ENERGY</span><br/><div style="margin-left: 30px;">Generate mask with zero weights for bins with the free energy greater than ENERGY.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">Determines differenciation scheme. Currently implemented schemes use either three or four points.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">Switch on periodicity for collective variables that are periodic.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: mask, gnuplot.</div><span style="color:purple; margin-left: 30px;">(Default: mask)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-integrate

2020-03-06T15:20:31Z

Maintenance script:

{{DISPLAYTITLE:abf-integrate}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-integrate]]
----
{{ABFUtils}}
<div style="text-align: center">abf-integrate: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-integrate</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname fename [fullfename]</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The program numericaly integrates data from the ABF calculation. The integration is performed either by reverse finite difference (RFD or RFD2) method, employing radial basis functions (RBF), or gaussian process (GPR).</p>

'''Arguments'''

<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname</span></span> Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fename</span></span> Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fullfename</span></span> Optional name of file with free energy surface containing all rigions (sampled and unsampled).</div>

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Integration method. Supported methods are: rfd (reverse finite differences via csparse), rfd2 (reverse finite differences via lapack), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--emethod NAME</span><br/><div style="margin-left: 30px;">Integration method for energy cut-off. Supported methods are: rfd (reverse finite differences via csparse), rfd2 (reverse finite differences via lapack), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), qr (QR factorization), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: RFD(LU,default), RFD2(QR,SVD,default), RBF(QR,SVD,default), and GPR(LU,SVD,SVD2,LL,default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">RFD2+RBF+GPR: Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--skipfftest</span><br/><div style="margin-left: 30px;">Skip flood fill test for discountinous regions.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-q, --energylimit NUMBER</span><br/><div style="margin-left: 30px;">Integrate data only if the free energy is below NUMBER. This limit enforces two integration runs. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--rmnegene</span><br/><div style="margin-left: 30px;">Remove regions with negative free energy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--skiplastelimit</span><br/><div style="margin-left: 30px;">Skip energy limit filter after final integration.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--mfmaxzscore NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Reject mean forces whose errors in prediction have z-score above NUMBER. In the test, it is assumend that mean force errors have zero mean and they follow normal distribution. This limit is aplied in the each pass. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfnumofztests NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Repeat z-score test for mean force errrors NUMBER times.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-c, --ncorr SPEC</span><br/><div style="margin-left: 30px;">GPR: Number of statistically correlated samples in the form NCorr1[xNCorr2x...]. The last value pads the rest. Split ncorr mode is enabled by the --splitncorr option.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--splitncorr</span><br/><div style="margin-left: 30px;">Use indepenedent ncorr for each CV.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: Factors influencing widths of RBFs or square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file with GPR hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-t, --rfac SPEC</span><br/><div style="margin-left: 30px;">RBF: Reduction factor for number of RBFs. Number of RBFs in given direction is number of bins in that direction divided by this factor in the form RFac1[xRFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-g, --overhang NUMBER</span><br/><div style="margin-left: 30px;">RBFs overhang to properly integrate areas near sampled edges. Ignored for periodic CVs.</div><span style="color:purple; margin-left: 30px;">(Default: 2)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includeglued</span><br/><div style="margin-left: 30px;">RBF+GPR: Explicitly include glued regions. This options is set ON when --glueing > 0.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--glueing NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled bins in close vicinity to sampled ones.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--glueholes</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled regions inside the FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">RFD: Switch on periodicity for collective variables that are periodic.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--userealglbmin</span><br/><div style="margin-left: 30px;">RBF+GPR: ignore --globalmin in the final integration step</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate free energy errors.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noenergy</span><br/><div style="margin-left: 30px;">GPR: Skip calculation of energy and errors (it can save some time when only logML is required).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--saveabf NAME</span><br/><div style="margin-left: 30px;">Save the final ABF accumulator into the file with NAME.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">RBF+GPR: name of file with input and predicted mean forces.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print the free energy surface. Supported formats are: plain, gnuplot, fes.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--oldrfd</span><br/><div style="margin-left: 30px;">RFD: Use old RFD implementation.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">RFD: Determine number of points employed in differenciation scheme (three or four is upported) in RFD method.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">GPR: Use numerical differentiation of kernel function (for testing only).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">GPR: Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">GPR: Calculate logPL.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">GPR: Include zero-point energy at position specified by --globalmin.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fasterror</span><br/><div style="margin-left: 30px;">GPR: Use faster algorithm for error calculation.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--keepcvs SPEC</span><br/><div style="margin-left: 30px;">Which CVs should be kept during statistical reweighting of FES. Flags are specified in the form CV1[xCV2x...] with F and T for skip and kept CV, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: T)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--reducedfes NAME</span><br/><div style="margin-left: 30px;">Name of file for FES reduced by statistical reweighting containing only kept CVs.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--temperature NUMBER</span><br/><div style="margin-left: 30px;">Absolute temperature for reduction of FES in [K].</div><span style="color:purple; margin-left: 30px;">(Default: 300)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-derivatives

2020-03-06T15:20:30Z

Maintenance script:

{{DISPLAYTITLE:abf-derivatives}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-derivatives]]
----
{{ABFUtils}}
<div style="text-align: center">abf-derivatives: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-derivatives</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-derivatives</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">dname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;"><span style="font-style: bold;">abf-derivatives</span> prints selected derivatives of the free energy with respect to given collective variables (mean forces) from the ABF accumulator.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">dname</span><br/><div style="margin-left: 30px;">Name of file where results will be printed. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit LIMIT</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-c, --ncorr NUMBER</span><br/><div style="margin-left: 30px;">Number of statistically correlated samples.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-i, --item CV</span><br/><div style="margin-left: 30px;">Forces for all CVs are printed (item == 0) unless item is set for given CV index (counted from 1).</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigma</span><br/><div style="margin-left: 30px;">Print the standard deviation of instanteous forces (fluctuations).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-e, --error</span><br/><div style="margin-left: 30px;">Print the standard deviation of mean forces (standard error).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--nognuplot</span><br/><div style="margin-left: 30px;">Do not print delimiters between records.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print results.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-combine

2020-03-06T15:20:29Z

Maintenance script:

{{DISPLAYTITLE:abf-combine}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-combine]]
----
{{ABFUtils}}
<div style="text-align: center">abf-combine: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-combine</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-combine</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accu1</span> <span style="color: purple;">accu2</span> <span style="color: purple;">output</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It combines two ABF accumulators into one. Both input accumulators have to be of the same dimensions.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accu1</span><br/><div style="margin-left: 30px;">Name of file with the first ABF accumulator. If the name is '-' then the accumulator is read from the standard input. The standard input can be used for accu1 or accu2 but not for both.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">accu2</span><br/><div style="margin-left: 30px;">Name of file with the second ABF accumulator. If the name is '-' then the accumulator is read from the standard input. The standard input can be used for accu1 or accu2 but not for both.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">output</span><br/><div style="margin-left: 30px;">Name of file where the result will be writen. If the name is '-' then the output will be written to the standard output.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--operation OP</span><br/><div style="margin-left: 30px;">Aritihmetic operation used in the accumulator combination. Supported operations are: 'add' and 'sub'</div><span style="color:purple; margin-left: 30px;">(Default: add)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-admin

2020-03-06T15:20:28Z

Maintenance script:

{{DISPLAYTITLE:abf-admin}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-admin]]
----
{{ABFUtils}}
<div style="text-align: center">abf-admin: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-admin</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">abf://server[:port]/command</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the multiple walkers extension of the ABF method.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">abf://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info = print information about registered clients<br />flush = save the accumulated ABF data on the server side<br />get?file=NAME = get the accumulated ABF data and saves them locally to the NAME file (the default name is _abfserver.rst)<br />shutdown = stop the server execution (use --force to skip protection by passphrase)<br />errors = print errors from the server stack</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-f, --force</span><br/><div style="margin-left: 30px;">Skip protection of server shutdown by passphrase.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}

Abf-accuinfo

2020-03-06T15:19:50Z

Maintenance script:

{{DISPLAYTITLE:abf-accuinfo}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-accuinfo]]
----
{{ABFUtils}}
<div style="text-align: center">abf-accuinfo: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''

<span style="margin-left: 15px;">abf-accuinfo</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">abf-accuinfo</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">It prints info about the ABF accumulator file. It lists collective variables and sampled area.</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">accuname</span><br/><div style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
|}