abp-energy

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abp-energy: version 6.380.1d87074 (2021-07-26 16:36)

Name

abp-energy

Synopsis

abp-energy [OPTIONS] [--] input output

Description

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

Arguments

input Name of file containing the ABP 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

-m, --mode NAME Energy calculation mode: mollified (use raw mollified FES), rl (Lucy-Richardson deconvolution) (Default: rl)

--rliter NUMBER Number of Lucy-Richardson deconvolution iteration. (Default: 10)

--floating Keep FES floating.

-l, --limit NUMBER Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 0)

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

--printall Print results for all bins even if not properly sampled.

--unsampledasmax Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.

--maxenergy NUMBER If set, this is the energy used of unsampled regions. (Default: 0)

--includebinstat Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.

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

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