ABF Utilities

abf-mask: version 5.271.40980cf (2020-03-02 15:18)

Name

abf-mask

Synopsis

abf-mask [OPTIONS] [--] accuname mask

Description

It create the ABF accumulator mask according to user specified criteria.

Arguments

accuname

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

mask

Name of file where the info about samples will be printed. If the name is '-' then the output will be written to the standard output.

Options

-m, --maxene ENERGY

Generate mask with zero weights for bins with the free energy greater than ENERGY.

(Default: 0)

-l, --limit NUMBER

Only bins containing more samples than NUMBER are considered as properly sampled.

(Default: 100)

--fdpoints NUMBER

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.

--output FORMAT

Output FORMAT, which will be used to print free energy surface. Supported formats are: mask, gnuplot.

(Default: mask)

-v, --verbose

Increase output verbosity.

--version

Output version information and exit.

-h, --help

Display this help and exit.