PMFLib Wiki - Recent changes [en]

Constrained Dynamics

Kulhanek — Sun, 21 Jun 2026 10:24:22 GMT

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	----		----
	=Introduction=		=Introduction=
	The CST method implemented in the PMFLib toolkit provides constrained molecular dynamics along selected collective variables (CVs). It can be used to ~~keep~~ one or more CVs at prescribed values, which allows the system to explore rare or otherwise poorly sampled regions of the configurational space. CST constraints can also be coupled with managed paths, ~~where~~ selected CST collective variables ~~define~~ the position of the system along a predefined path. In addition to enforcing constraints, the method supports free energy calculations based on the Blue Moon formalism and vector field approaches. The calculated free energy profile can be further decomposed into internal energy and entropic contributions, providing a more detailed thermodynamic description of the studied process.		The CST method implemented in the PMFLib toolkit provides constrained molecular dynamics along selected collective variables (CVs). It can be used to maintain one or more CVs at prescribed values, which allows the system to explore rare or otherwise poorly sampled regions of the configurational space. CST constraints can also be coupled with managed paths, in which selected CST collective variables determine the position of the system along a predefined path. In addition to enforcing constraints, the method supports free energy calculations based on the Blue Moon formalism and vector-field approaches. The calculated free energy profile can be further decomposed into internal energy and entropic contributions, providing a more detailed thermodynamic description of the studied process.

	=Documentation=		=Documentation=

Collective Variable Monitoring

Kulhanek — Sun, 21 Jun 2026 10:20:07 GMT

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	----		----
	=Introduction=		=Introduction=
	The Collective Variable Monitoring (MON) method implemented in PMFLib ~~is used to record~~ the values of selected collective variables during a molecular dynamics simulation. The generated time series can be used for further analysis, such as plotting the time evolution of collective variables, checking the stability of a simulation, or estimating statistical properties including autocorrelation times. This method ~~does not apply any~~ bias or constraint to the system; it only monitors and writes the selected collective variables for subsequent processing.		The Collective Variable Monitoring (MON) method implemented in PMFLib records the values of selected collective variables during a molecular dynamics simulation. The generated time series can be used for further analysis, such as plotting the time evolution of collective variables, checking the stability of a simulation, or estimating statistical properties including autocorrelation times. This method imposes no bias or constraint on the system; it only monitors and writes the selected collective variables for subsequent processing.

	=Documentation=		=Documentation=

Path Driving

Kulhanek — Sun, 21 Jun 2026 10:18:47 GMT

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	----		----
	=Introduction=		=Introduction=
	The Path Driving method implemented in PMFLib ~~is used to guide~~ a molecular system along a predefined path in the space of collective variables. Such a path can represent, for example, an ~~optimized~~ reaction or transition pathway obtained by the string method. By driving the system along this path, PDRV ~~makes it possible to explore~~ structural changes ~~associated with~~ different positions on the path and ~~to generate~~ representative configurations for further analysis. The method is also useful for preparing initial restart files for individual beads of the string method before the actual path ~~optimization is started~~, ensuring that the subsequent ~~optimization begins~~ from physically relaxed structures distributed along the ~~desired~~ transition route.		The Path Driving method implemented in PMFLib guides a molecular system along a predefined path in the space of collective variables. Such a path can represent, for example, an optimised reaction or transition pathway obtained by the string method. By driving the system along this path, PDRV enables exploration of structural changes at different positions along the path and generation of representative configurations for further analysis. The method is also useful for preparing initial restart files for individual beads in the string method before the actual path optimisation begins, ensuring that the subsequent optimisation starts from physically relaxed structures distributed along the studied transition route.

	=Documentation=		=Documentation=

Restrained Dynamics

Kulhanek — Sun, 21 Jun 2026 10:13:13 GMT

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	Navigation: [[Documentation]] / [[Methods]] / [[Restrained Dynamics]]		Navigation: [[Documentation]] / [[Methods]] / [[Restrained Dynamics]] __NOEDITSECTION__
	----		----
	~~__NOEDITSECTION__~~		=Introduction=
	==~~Contents~~==		The RST module implemented in the PMFLib toolkit provides restrained molecular dynamics along selected collective variables (CVs). It can be used to apply individual restraints that keep one or more CVs close to their prescribed values, thereby allowing the system to sample selected regions of the configurational space more efficiently. RST restraints can also be coupled with managed paths, in which selected collective variables determine the position of the system along a predefined path. In addition to static restraints, the module supports driving along CVs or paths, making it suitable for generating initial configurations, exploring transitions, or preparing umbrella sampling simulations. Free energy profiles from restrained simulations can be reconstructed using the WHAM method with third-party software.
	* [[Restrained Dynamics#Description\|RST:Description]]
			=Documentation=
	* [[RST:Controls]]		* [[RST:Controls]]
	* [[RST:Restraints]]		* [[RST:Restraints]]
			* [[RST:Files]]
			* [[RST:Utilities]]
	* [[RST:Examples]]		* [[RST:Examples]]
	* [[RST:Post-processing]]
	* [[RST:Utilities]]

	==~~Description~~==
			===References===

ABP:Files

Kulhanek — Sun, 21 Jun 2026 09:54:46 GMT

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	Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Files]]		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Files]] __NOEDITSECTION__
	----		----

			==[files]==
			{\| style="width: 100%;"
			\| style="width: 10em;" \| '''Key'''
			\| style="width: 10em;" \| '''Default value'''
			\| style="width: 5em;" \| '''Type'''
			\| '''Description'''
			\|- style="vertical-align: top; background-color: #f6f6f6;"
			\| fabpdef
			\| {ABP}
			\| [[Control key types\|string]]
			\| Specifies either a PRMFile group or the name of a file containing the specification of collective variables used by the ABP method.
			\|- style="vertical-align: top;"
			\| fabpout
			\| _abp.out
			\| [[Control key types\|string]]
			\| Specifies the file name used for output from ABP simulations. This file contains status information and the time evolution of collective variables.
			\|- style="vertical-align: top; background-color: #f6f6f6;"
			\| fabprst
			\| _abp.rst
			\| [[Control key types\|string]]
			\| Specifies the name of the file containing accumulated results from ABP simulations.
			\|- style="vertical-align: top;"
			\| fabptrj
			\| _abp.trj
			\| [[Control key types\|string]]
			\| Specifies the name of the file containing the time evolution of accumulated ABP results.
			\|}

General setup

Kulhanek — Sun, 21 Jun 2026 09:52:01 GMT

Show changes

STM:Collective variables

Kulhanek — Sat, 20 Jun 2026 13:30:16 GMT

Replaced content with "STM:Collective Variables"

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	~~Navigation: [[Documentation]] / [[Methods]] / [[String Method]] / [[STM:Client]] /~~ [[STM:~~Collective variables]]~~		[[STM:Collective Variables]]
	~~----~~
	~~__NOEDITSECTION__ __NOTOC__~~
	Each collective variable used in a string method simulation is specified in a separate [CV] section. These sections are placed either in a special group, {STM} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled by the fstmdef option in the [[General setup#.5Bfiles.5D\|<nowiki>[files]</nowiki>]] section.

	~~==[CV]==~~
	~~{\| style="width: 100%;"~~
	~~\| style="width: 10em;" \| '''Key'''~~
	~~\| style="width: 10em;" \| '''Default value'''~~
	~~\| style="width: 5em;" \| '''Type'''~~
	~~\| '''Description'''~~
	~~\|- style="vertical-align: top; background-color: #f6f6f6;"~~
	~~\| '''name'''~~
	\|
	~~\| [[Control key types\|string]]~~
	~~\| The name of collective variable from the list of general collective variables. For details, see: [[~~ Collective Variables]]~~. The CV cannot be a member of [[managed path]].~~
	~~\|- style="vertical-align: top;"~~
	~~\| '''force_constant'''~~
	\|
	~~\| [[Control key types\|real]]~~
	~~\| The force constant that will be used to fix the collective variable.~~
	\|}
	~~''Keys in bold are mandatory.''~~

	~~'''NOTE:''' Collective variables must be provided in the same order in which they are defined on the string server!~~

STM:Client

Kulhanek — Sat, 20 Jun 2026 13:30:03 GMT

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	==Configuration==		==Configuration==
	* [[STM:Client Controls]]		* [[STM:Client Controls]]
	* [[STM:Collective ~~variables~~]]		* [[STM:Collective Variables]]

	==IMPORTANT==		==IMPORTANT==

STM:Collective Variables

Kulhanek — Sat, 20 Jun 2026 13:29:51 GMT

Created page with "Navigation: Documentation / Methods / String Method / STM:Client / STM:Collective Variables ---- __NOEDITSECTION__ __NOTOC__ Each collective variable used in a string method simulation is specified in a separate [CV] section. These sections are placed either in a special group, {STM} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled..."

New page

Navigation: [[Documentation]] / [[Methods]] / [[String Method]] / [[STM:Client]] / [[STM:Collective Variables]]
----
__NOEDITSECTION__ __NOTOC__
Each collective variable used in a string method simulation is specified in a separate [CV] section. These sections are placed either in a special group, {STM} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled by the fstmdef option in the [[General setup#.5Bfiles.5D|<nowiki>[files]</nowiki>]] section.

==[CV]==
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''
| style="width: 10em;" | '''Default value'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
| '''name'''
|
| [[Control key types|string]]
| The name of collective variable from the list of general collective variables. For details, see: [[ Collective Variables]]. The CV cannot be a member of [[managed path]].
|- style="vertical-align: top;"
| '''force_constant'''
|
| [[Control key types|real]]
| The force constant that will be used to fix the collective variable.
|}
''Keys in bold are mandatory.''

'''NOTE:''' Collective variables must be provided in the same order in which they are defined on the string server!

String Method

Kulhanek — Sat, 20 Jun 2026 13:29:41 GMT

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	* [[STM:Client]]		* [[STM:Client]]
	** [[STM:Client Controls]]		** [[STM:Client Controls]]
	** [[STM:Collective ~~variables~~]]		** [[STM:Collective Variables]]
	* [[STM:Post-processing]]		* [[STM:Post-processing]]
	* [[STM:Utilities]]		* [[STM:Utilities]]

Adaptive Biasing Potential Method

Kulhanek — Sat, 20 Jun 2026 13:27:10 GMT

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	----		----
	=Introduction=		=Introduction=
	The Adaptive Biasing Potential (ABP) method implemented in PMFLib follows the mollified density-of-states formulation [1]. During the simulation, ~~the method accumulates a smoothed population of~~ the selected collective variables ~~and uses it~~ to construct an adaptive biasing force. The directly obtained free-energy estimate is therefore the mollified free energy, not the exact free energy surface. To recover the final free energy, the mollification error must be removed by post-processing, typically via deconvolution. In PMFLib, this correction and reconstruction of the free-energy profile are performed with the [[abp-energy]] utility.		The Adaptive Biasing Potential (ABP) method implemented in PMFLib follows the mollified density-of-states formulation [1]. During the simulation, ABP uses the selected collective variables to construct a discretised, mollified population, which is then used to compute the mollified free energy and the corresponding adaptive biasing force. The directly obtained free-energy estimate is therefore the mollified free energy, not the exact free-energy surface. To recover the final free energy, the mollification error must be removed by post-processing, typically via deconvolution. In PMFLib, this correction and reconstruction of the free-energy profile are performed with the [[abp-energy]] utility. ABP also supports the Multiple-Walker Approach, in which several simulations contribute to a shared accumulator through the MWA server, accelerating the construction of the mollified population and the convergence of the adaptive bias.

	=Documentation=		=Documentation=

ABP:Collective Variables

Kulhanek — Sat, 20 Jun 2026 13:24:25 GMT

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	Navigation: [[Documentation]] / [[Methods]] / [[~~Constrained Dynamics~~]] / [[~~CST~~:~~Constraints~~]] __NOEDITSECTION__ __NOTOC__		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Collective Variables]] __NOEDITSECTION__ __NOTOC__
	----		----
	Each collective variable employed by the Adaptive Biasing Potential (ABP) method is provided in a separate [CV] section. These sections are placed either in a special group, {ABP} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled by the fabpdef option in the [[General setup#.5Bfiles.5D\|<nowiki>[files]</nowiki>]] section.		Each collective variable employed by the Adaptive Biasing Potential (ABP) method is provided in a separate [CV] section. These sections are placed either in a special group, {ABP} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled by the fabpdef option in the [[General setup#.5Bfiles.5D\|<nowiki>[files]</nowiki>]] section.

	The ABP method uses the selected collective variables to build a discretized mollified population. This population is then used to calculate the mollified free energy and the corresponding adaptive biasing force. Since the obtained free-energy surface is mollified, the final free energy should be corrected by deconvolution using the [[abp-energy]] utility.

	==[CV]==		==[CV]==
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	\|		\|
	\| [[Control key types\|real]]		\| [[Control key types\|real]]
	\| The maximum value of the CV range. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory and its value must be greater than <i>min_value</i>.		\| The maximum value of the CV range. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory, and its value must be greater than <i>min_value</i>.
	\|- style="vertical-align: top;"		\|- style="vertical-align: top;"
			\| '''nbins'''
			\|
			\| [[Control key types\|integer]]
			\| The number of bins used to discretise the CV range between <i>min_value</i> and <i>max_value</i>. This key is mandatory, and its value must be greater than zero.
			\|- style="vertical-align: top; background-color: #f6f6f6;"
	\| '''width'''		\| '''width'''
	\|		\|
	\| [[Control key types\|real]]		\| [[Control key types\|real]]
	\| The width of the Gaussian mollifier used to smooth the population along this collective variable. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory ~~and its value must be greater than zero.~~		\| The width of the Gaussian mollifier used to smooth the population along this collective variable. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory, and its value must be greater than zero.
	~~\|- style="vertical-align: top; background-color: #f6f6f6;"~~
	~~\| '''nbins'''~~
	\|
	~~\| [[Control key types\|integer]]~~
	~~\| The number of bins used to discretize the CV range between <i>min_value</i> and <i>max_value</i>. This key is mandatory~~ and its value must be greater than zero.
	\|}		\|}

ABP:Collective Variables

Kulhanek — Sat, 20 Jun 2026 13:21:05 GMT

Created page with "Navigation: Documentation / Methods / Constrained Dynamics / CST:Constraints __NOEDITSECTION__ __NOTOC__ ---- Each collective variable employed by the Adaptive Biasing Potential (ABP) method is provided in a separate [CV] section. These sections are placed either in a special group, {ABP} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlle..."

New page

Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[CST:Constraints]] __NOEDITSECTION__ __NOTOC__
----
Each collective variable employed by the Adaptive Biasing Potential (ABP) method is provided in a separate [CV] section. These sections are placed either in a special group, {ABP} by default, when the collective variables are defined in the main control file, or in the {MAIN} group of a separate file. The name of the group or the file is controlled by the fabpdef option in the [[General setup#.5Bfiles.5D|<nowiki>[files]</nowiki>]] section.

The ABP method uses the selected collective variables to build a discretized mollified population. This population is then used to calculate the mollified free energy and the corresponding adaptive biasing force. Since the obtained free-energy surface is mollified, the final free energy should be corrected by deconvolution using the [[abp-energy]] utility.

==[CV]==
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''
| style="width: 10em;" | '''Default value'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
| '''name'''
|
| [[Control key types|string]]
| The name of a collective variable from the list of general collective variables. For details, see [[Collective Variables|Collective variables]].
|- style="vertical-align: top;"
| '''min_value'''
|
| [[Control key types|real]]
| The minimum value of the CV range. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory.
|- style="vertical-align: top; background-color: #f6f6f6;"
| '''max_value'''
|
| [[Control key types|real]]
| The maximum value of the CV range. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory and its value must be greater than min_value.
|- style="vertical-align: top;"
| '''width'''
|
| [[Control key types|real]]
| The width of the Gaussian mollifier used to smooth the population along this collective variable. The value is specified in the natural unit of the selected collective variable and is internally converted to PMFLib internal units. This key is mandatory and its value must be greater than zero.
|- style="vertical-align: top; background-color: #f6f6f6;"
| '''nbins'''
|
| [[Control key types|integer]]
| The number of bins used to discretize the CV range between min_value and max_value. This key is mandatory and its value must be greater than zero.
|}

''Keys in bold are mandatory.''

'''NOTE:''' A collective variable employed by the ABP method cannot be controlled by a [[managed path]] operating in driven mode.

ABP:Files

Kulhanek — Sat, 20 Jun 2026 07:53:20 GMT

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	Navigation: [[Documentation]] / [[Methods]] / [[~~Constrained Dynamics~~]] / [[ABP:Files]]		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Files]]
	----		----

ABP:Examples

Kulhanek — Sat, 20 Jun 2026 07:53:09 GMT

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	Navigation: [[Documentation]] / [[Methods]] / [[~~Constrained Dynamics~~]] / [[ABP:Examples]]		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Examples]]
	----		----

ABP:Files

Kulhanek — Sat, 20 Jun 2026 07:52:54 GMT

Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Files ----"

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Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[ABP:Files]]
----

ABP:Examples

Kulhanek — Sat, 20 Jun 2026 07:52:25 GMT

Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Examples ----"

New page

Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[ABP:Examples]]
----

ABP:Controls

Kulhanek — Sat, 20 Jun 2026 07:46:52 GMT

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	## Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential]] / [[ABP:Controls]]		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Controls]] __NOEDITSECTION__ __NOTOC__
			----
	~~NOEDITSECTION NOTOC~~

	The behaviour of the Adaptive Biasing Potential (ABP) method is controlled by the setup provided in the [abp] section. This section belongs to the {PMFLIB} group. The ABP method implemented in PMFLib calculates the mollified free energy from a smoothed population of selected collective variables. The obtained free-energy surface is therefore not the exact free energy and has to be corrected by deconvolution. This post-processing is performed by the [[abp-energy]] utility.		The behaviour of the Adaptive Biasing Potential (ABP) method is controlled by the setup provided in the [abp] section. This section belongs to the {PMFLIB} group. The ABP method implemented in PMFLib calculates the mollified free energy from a smoothed population of selected collective variables. The obtained free-energy surface is therefore not the exact free energy and has to be corrected by deconvolution. This post-processing is performed by the [[abp-energy]] utility.
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	\|		\|
	\| [[Control key types\|string]]		\| [[Control key types\|string]]
	\| The key file used to connect the ABP walker to an ~~ABP~~ server in the multiple-walkers setup. If the key is not provided, the multiple-walkers ABP mode is disabled. This option is available only if PMFLib was compiled with network support.		\| The key file used to connect the ABP walker to an MWA server in the multiple-walkers setup. If the key is not provided, the multiple-walkers ABP mode is disabled. This option is available only if PMFLib was compiled with network support.
	\|- style="vertical-align: top;"		\|- style="vertical-align: top;"
	\| fserverupdate		\| fserverupdate
	\| 500		\| 500
	\| [[Control key types\|integer]]		\| [[Control key types\|integer]]
	\| Every <i>fserverupdate</i> MD steps, the ABP walker exchanges accumulated data with the ABP server~~. This option is used only in the multiple-walkers setup~~.		\| Every <i>fserverupdate</i> MD steps, the ABP walker exchanges accumulated data with the ABP server.
	\|- style="vertical-align: top; background-color: #f6f6f6;"		\|- style="vertical-align: top; background-color: #f6f6f6;"
	\| fabortonmwaerr		\| fabortonmwaerr
	\| on		\| on
	\| [[Control key types\|logical]]		\| [[Control key types\|logical]]
	\| Disable/Enable abortion of the simulation if communication with the ~~ABP~~ server fails. If this option is disabled, the simulation can continue even after a multiple-walkers communication error.		\| Disable/Enable abortion of the simulation if communication with the MWA server fails. If this option is disabled, the simulation can continue even after a multiple-walkers communication error.
			\|- style="vertical-align: top;"
			\| fconrepeats
			\| 0
			\| [[Control key types\|integer]]
			\| The maximum number of repeated attempts to reconnect to the MWA server after a communication failure. If the number of failed attempts exceeds <i>fconrepeats</i>, the action depends on <i>fabortonmwaerr</i>: if it is enabled, the simulation is aborted; otherwise, the multiple-walkers ABP mode is disabled, and the simulation continues without server communication.
	\|}		\|}

ABP:Controls

Kulhanek — Sat, 20 Jun 2026 07:39:05 GMT

Created page with "## Navigation: Documentation / Methods / Adaptive Biasing Potential / ABP:Controls **NOEDITSECTION** **NOTOC** The behaviour of the Adaptive Biasing Potential (ABP) method is controlled by the setup provided in the [abp] section. This section belongs to the {PMFLIB} group. The ABP method implemented in PMFLib calculates the mollified free energy from a smoothed population of selected collective variables. The obtained free-energy surface is therefore no..."

New page

## Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential]] / [[ABP:Controls]]

**NOEDITSECTION** **NOTOC**

The behaviour of the Adaptive Biasing Potential (ABP) method is controlled by the setup provided in the [abp] section. This section belongs to the {PMFLIB} group. The ABP method implemented in PMFLib calculates the mollified free energy from a smoothed population of selected collective variables. The obtained free-energy surface is therefore not the exact free energy and has to be corrected by deconvolution. This post-processing is performed by the [[abp-energy]] utility.

==[abp]==
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''
| style="width: 10em;" | '''Default value'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
| fmode
| 0
| [[Control key types|integer]]
| The mode of the Adaptive Biasing Potential method: 0 - the method is disabled 1 - the method is enabled If the method is enabled, at least one collective variable has to be provided for ABP sampling.
|- style="vertical-align: top;"
| fhbias
| 3.0
| [[Control key types|real]]
| The bias height used to control the strength of the adaptive biasing potential. The value is provided in the currently selected energy unit.
|- style="vertical-align: top; background-color: #f6f6f6;"
| feimode
| 1
| [[Control key types|integer]]
| The extrapolation/interpolation mode used for the ABP force evaluation: 1 - linear ramp mode
|- style="vertical-align: top;"
| fhramp
| 10
| [[Control key types|integer]]
| The ramp size used in the linear ramp mode. The ramp reduces the ABP force in poorly sampled regions and gradually switches it on as the local mollified population increases.
|- style="vertical-align: top; background-color: #f6f6f6;"
| fsample
| 5000
| [[Control key types|integer]]
| Every fsample MD steps, the accumulated ABP data will be printed to the ABP output file. The name of the output file is provided in the [[General setup|[files]]] section. If fsample is zero, the regular output is disabled.
|- style="vertical-align: top;"
| frestart
| off
| [[Control key types|logical]]
| Disable/Enable restarting the ABP simulation from the previous run. The name of the restart file is provided in the [[General setup|[files]]] section.
|- style="vertical-align: top; background-color: #f6f6f6;"
| frstupdate
| 5000
| [[Control key types|integer]]
| Every frstupdate MD steps, the ABP restart file will be written. If frstupdate is zero, periodic writing of the restart file is disabled.
|- style="vertical-align: top;"
| ftrjsample
| 0
| [[Control key types|integer]]
| Every ftrjsample MD steps, the ABP accumulator is written to the ABP trajectory file. This file can be used to analyse the evolution of the mollified free-energy estimate. If ftrjsample is zero, the trajectory output is disabled.
|}

==[abp-walker]==
{| style="width: 100%;"
| style="width: 10em;" | '''Key'''
| style="width: 10em;" | '''Default value'''
| style="width: 5em;" | '''Type'''
| '''Description'''
|- style="vertical-align: top; background-color: #f6f6f6;"
| fserverkey
|
| [[Control key types|string]]
| The key file used to connect the ABP walker to an ABP server in the multiple-walkers setup. If the key is not provided, the multiple-walkers ABP mode is disabled. This option is available only if PMFLib was compiled with network support.
|- style="vertical-align: top;"
| fserverupdate
| 500
| [[Control key types|integer]]
| Every fserverupdate MD steps, the ABP walker exchanges accumulated data with the ABP server. This option is used only in the multiple-walkers setup.
|- style="vertical-align: top; background-color: #f6f6f6;"
| fabortonmwaerr
| on
| [[Control key types|logical]]
| Disable/Enable abortion of the simulation if communication with the ABP server fails. If this option is disabled, the simulation can continue even after a multiple-walkers communication error.
|}

ABP:Utilities

Kulhanek — Sat, 20 Jun 2026 07:32:33 GMT

← Older revision		Revision as of 07:32, 20 June 2026
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	Navigation: [[Documentation]] / [[Methods]] / [[~~Constrained Dynamics~~]] / [[ABP:Utilities]] __NOEDITSECTION__		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] / [[ABP:Utilities]] __NOEDITSECTION__
	----		----
	The ~~CST~~ data can be processed by the following utilities.		The ABP data can be processed by the following utilities.
	* ~~CST~~ accumulator processing ~~(only if <i>freadranges</i> is <i>on</i>)~~.		* ABP accumulator processing.
	** [[accu-info]]		** [[accu-info]]
	** [[accu-combine]]		** [[accu-combine]]
	** [[accu-trajectory]]		** [[accu-trajectory]]
	* ~~The free energy, internal~~ energy~~, entropic contribution and other data~~:		* MWA (Multiple Walker Approach)
	** [[~~pmf~~-~~integrate~~]]		** [[mwa-server]]
			** [[mwa-admin]]
			* Free energy:
			** [[abp-energy]]

ABP:Utilities

Kulhanek — Sat, 20 Jun 2026 07:30:27 GMT

Created page with "Navigation: Documentation / Methods / Constrained Dynamics / ABP:Utilities __NOEDITSECTION__ ---- The CST data can be processed by the following utilities. * CST accumulator processing (only if freadranges is on). ** accu-info ** accu-combine ** accu-trajectory * The free energy, internal energy, entropic contribution and other data: ** pmf-integrate"

New page

Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[ABP:Utilities]] __NOEDITSECTION__
----
The CST data can be processed by the following utilities.
* CST accumulator processing (only if freadranges is on).
** [[accu-info]]
** [[accu-combine]]
** [[accu-trajectory]]
* The free energy, internal energy, entropic contribution and other data:
** [[pmf-integrate]]

CST:Utilities

Kulhanek — Sat, 20 Jun 2026 07:29:08 GMT

← Older revision		Revision as of 07:29, 20 June 2026
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	Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[CST:Utilities]] __NOEDITSECTION__		Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[CST:Utilities]] __NOEDITSECTION__
	----		----
	~~{{CSTUtils}}~~		The CST data can be processed by the following utilities.
	The CST data can be processed be the following utilities.
	* CST accumulator processing (only if <i>freadranges</i> is <i>on</i>).		* CST accumulator processing (only if <i>freadranges</i> is <i>on</i>).
	** [[accu-info]]		** [[accu-info]]

Adaptive Biasing Potential Method

Kulhanek — Sat, 20 Jun 2026 07:27:08 GMT

← Older revision		Revision as of 07:27, 20 June 2026
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	Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]]		Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Potential Method]] __NOEDITSECTION__
	----		----
	~~__NOEDITSECTION__~~		=Introduction=
	~~==Contents~~==		The Adaptive Biasing Potential (ABP) method implemented in PMFLib follows the mollified density-of-states formulation [1]. During the simulation, the method accumulates a smoothed population of the selected collective variables and uses it to construct an adaptive biasing force. The directly obtained free-energy estimate is therefore the mollified free energy, not the exact free energy surface. To recover the final free energy, the mollification error must be removed by post-processing, typically via deconvolution. In PMFLib, this correction and reconstruction of the free-energy profile are performed with the [[abp-energy]] utility.
	* [[Adaptive Biasing Potential ~~Method#Description\|~~ABP~~:Description~~]]
			=Documentation=
	* [[ABP:Controls]]		* [[ABP:Controls]]
	* [[ABP:Collective ~~variables~~]]		* [[ABP:Collective Variables]]
	* [[ABP:~~Post-processing~~]]		* [[ABP:Multiple Walker Approach]]
	* [[ABP:~~Multiple walkers approach~~]]		* [[ABP:Files]]
	* [[ABP:Utilities]]		* [[ABP:Utilities]]
	* [[ABP:Examples]]		* [[ABP:Examples]]


	==~~Description~~==		===References===
			(1) Dickson, B. M.; Legoll, F.; Lelièvre, T.; Stoltz, G.; Fleurat-Lessard, P. Free Energy Calculations: An Efficient Adaptive Biasing Potential Method. <i>J. Phys. Chem. B</i> <b>2010</b>, <i>114 (17)</i>, 5823–5830. [https://doi.org/10.1021/jp100926h https://doi.org/10.1021/jp100926h].

CST:Files

Kulhanek — Sat, 20 Jun 2026 07:01:59 GMT

Created page with "Navigation: Documentation / Methods / Constrained Dynamics / CST:Files ----"

New page

Navigation: [[Documentation]] / [[Methods]] / [[Constrained Dynamics]] / [[CST:Files]]
----

Constrained Dynamics

Kulhanek — Sat, 20 Jun 2026 07:01:43 GMT

← Older revision		Revision as of 07:01, 20 June 2026
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	* [[CST:Controls]]		* [[CST:Controls]]
	* [[CST:Constraints]]		* [[CST:Constraints]]
			* [[CST:Files]]
	* [[CST:Utilities]]		* [[CST:Utilities]]
	* [[CST:Examples]]		* [[CST:Examples]]

	===References===		===References===