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{{DISPLAYTITLE:mtd-energy}} | |||
Navigation: [[Documentation]] / [[Utilities]] / [[mtd-energy]] | |||
Navigation: [[Documentation]] / [[ | |||
---- | ---- | ||
<div style="text-align: center">mtd-energy: version 6.380.1d87074 (2021-07-26 16:36)</div>'''Name''' | |||
'''Name''' | |||
mtd-energy | <span style="margin-left: 15px;">mtd-energy</span> | ||
'''Synopsis''' | '''Synopsis''' | ||
<span style="color: maroon;">mtd-energy</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">input output </span> | <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''' | '''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''' | '''Arguments''' | ||
{| style="margin-left: 2em; width: | {| 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/> | | <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/> | | <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;">- | |<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;">-- | |<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;">-- | |<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;">-- | |<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;">-- | |<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; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-- | |<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;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-- | |<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; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-- | |<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;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">-- | |<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;">-v, --verbose</span><br/>< | |<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;" | |- style="vertical-align: top; background-color: #e6e6e6;" | ||
|<span style="color: blue;">--version</span><br/>< | |<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div> | ||
|- style="vertical-align: top; " | |- style="vertical-align: top;" | ||
|<span style="color: blue;">-h, --help</span><br/>< | |<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div> | ||
|} | |} | ||
Latest revision as of 13:45, 28 July 2021
Navigation: Documentation / Utilities / mtd-energy
mtd-energy: version 6.380.1d87074 (2021-07-26 16:36)
Name
mtd-energy
Synopsis
mtd-energy [OPTIONS] [--] input output
Description
mtd-energy calculates the free energy surface estimate from the MTD accumulator file.
Arguments
| input Input file name containing the MTD accumulator or trajectory file with MTD accumulators or '-' to read data from the standard input.
|
| output Output file name for the free energy surface or '-' to write data to the standard output.
|
Options
| --floating Keep FES floating.
|
| -s, --smooth NUMBER Calculate average from specified number of MTD accumulators counted from the end of the trajectory file. (Default: 1)
|
| -l, --limit NUMBER Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 0)
|
| -o, --offset NUMBER Specify an integration constant. (Default: 0)
|
| --printall Print results for all bins even if not properly sampled.
|
| --unsampledasmax Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.
|
| --maxenergy NUMBER If set, this is the energy used of unsampled regions. (Default: 0)
|
| --includebinstat Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.
|
| --output FORMAT Output FORMAT, which will be used to print free energy surface. Supported formats are: plain and gnuplot. (Default: gnuplot)
|
| --noheader Do not print header to output file.
|
| --fx FORMAT Output FORMAT, which will be used to print values of collective variables. (Default: %15.7le)
|
| --fe FORMAT Output FORMAT, which will be used to print values of free energy. (Default: %15.7le)
|
| --fs FORMAT Output FORMAT, which will be used to print values of standard deviations. (Default: %15.7le)
|
| -v, --verbose Increase output verbosity.
|
| --version Output version information and exit.
|
| -h, --help Display this help and exit.
|