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Mtd-energy (view source)

Revision as of 13:45, 28 July 2021

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{{DISPLAYTITLE:mtd-energy}}
{{DISPLAYTITLE:mtd-energy}}
Navigation: [[Documentation]] / [[Methods]] / [[Metadynamics]] / [[MTD:Utilities]] / [[mtd-energy]]
Navigation: [[Documentation]] / [[Utilities]] / [[mtd-energy]]
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{{MTDUtils}}
<div style="text-align: center">mtd-energy: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name'''
<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>
<span style="margin-left: 15px;">mtd-energy</span>
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'''Description'''
'''Description'''


<p style="text-indent: 1em; text-align: justify;">It calculate the free energy surface estimate from the metadynamics restart file.</p>
<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'''
'''Arguments'''
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{| style="margin-left: 2em; width: 95%;"
{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|- 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>
| <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;"
|- 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>
| <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>
|}
|}


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{| style="margin-left: 2em; width: 95%;"
{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|- 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>
|<span style="color: blue;">--floating</span><br/><div style="margin-left: 30px;">Keep FES floating.</div>
|- style="vertical-align: top;"
|- 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>
|<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;"
|- 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>
|<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;"
|- 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>
|<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;"
|- 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>
|<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;"
|- style="vertical-align: top;"
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to output file.</div>
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