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Navigation: Documentation / Methods / Metadynamics / MTD:Utilities / mtd-energy

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MTD Utilities

• mtd-admin
• mtd-energy
• mtd-server

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

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.

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.