Revision as of 12:30, 11 April 2016

MTD Utilities

Name

mtd-energy

Synopsis

mtd-energy [OPTIONS] [--] input output

Description

It calculate the free energy surface estimate from the metadynamics restart file.

Arguments

input

Name of file containing the metadynamics restart file. If the name is '-' then the file is read from the standard input.

output

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.

Options

-t, --time NUMBER
Specifies metadynamics time that will be used for the energy calculation.

(Default: 0)

--offset REAL
Determine position of global minima.

(Default: 0)

--smooth NUMBER
Calculate the energy surface average from time interval SMOOTH to TIME.

(Default: 0)

--sd
Print the standard deviation of the free energy when the smoothing is enabled.

--output FORMAT
Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.

(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.

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 <span 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.</span>
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 <span 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.</span>
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 '''Options'''
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-Laio, A.; Gervasio, F. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. ''REPORTS ON PROGRESS IN PHYSICS'' '''2008''', ''71 (12)'', doi: 10.1088/0034-4885/71/12/126601.