ABF Utilities

Name

abf-integrate

Synopsis

abf-integrate [OPTIONS] [--] accuname fename

Description

It numericaly integrates data from the ABF calculation. The integration is performed by reverse finite difference method with order either 3 or 4.

Arguments

accuname

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

fename

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

-l, --limit NUMBER
Only bins containing more samples than NUMBER are considered as properly sampled.
(Default: 100)

--fdorder ORDER
Determines differenciation scheme. Currently implemented schemes use either three or four points.
(Default: 3)

-o, --offset NUMBER
Specify an integration constant.
(Default: 0)

-p, --periodic
Switch on periodicity for collective variables that are periodic.

-e, --errors
Integrate errors of derivatives.

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

--printwithlimit
Print results from bins that were adequately sampled.

--noheader
Do not print header to the output file.

--fx FORMAT
Output FORMAT, which will be used to print values of collective variables.
(Default: %15.7e)

--fe FORMAT
Output FORMAT, which will be used to print values of free energy.
(Default: %15.7e)

-v, --verbose
Increase output verbosity.

--version
Output version information and exit.

-h, --help
Display this help and exit.

Abf-integrate