Abf-mask

Navigation: Documentation / Methods / Adaptive Biasing Force Method / ABF:Utilities / abf-mask

---

ABF Utilities

• abf-accuinfo
• abf-admin
• abf-combine
• abf-derivatives
• abf-integrate
• abf-mask
• abf-optgprhyprms
• abf-samples
• abf-server
• abf-trajectory

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)

--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.

--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.