Command line tool: drr_tool

Module	drr
Description	Input
Extract or merge the drrstate files.	command line args

Details

• Extract .grad and .count files from the binary output .drrstate
• Merge windows

Examples

The following command will extract .grad and .count files.

plumed drr_toolExtract or merge the drrstate files. This action has hidden defaults. More details --extractExtract drrstate file(s) eabf.drrstate

The drr_tool action with label plumed calculates somethingplumed drr_toolExtract or merge the drrstate files. This action uses the defaults shown here. More details --extractExtract drrstate file(s) eabf.drrstate
 --dump-fmt the format to use to dump the output %%f --units the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol kj/mol 

The following command will merge windows of two .drrstate file, and output the .grad and .count files.

plumed drr_toolExtract or merge the drrstate files. This action has hidden defaults. More details --mergeMerge eABF windows win1.drrstate,win2.drrstate

The drr_tool action with label plumed calculates somethingplumed drr_toolExtract or merge the drrstate files. This action uses the defaults shown here. More details --mergeMerge eABF windows win1.drrstate,win2.drrstate
 --dump-fmt the format to use to dump the output %%f --units the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol kj/mol 

After getting the .grad and .count file, you can do numerical integration by using abf_integrate tool from https://github.com/Colvars/colvars/tree/master/colvartools

abf_integrate eabf.czar.grad

units

The abf_integrate in colvartools is in kcal/mol, so it may be better to use --units kcal/mol when running drr_tool

Syntax

The following table describes the command line options that are available for this tool

Keyword	Description
--help/-h	print this help
--extract	Extract drrstate file(s)
--merge	Merge eABF windows
--merge_output	The output filename of the merged result
--divergence	Calculate divergence of gradient field (experimental)
--dump-fmt	the format to use to dump the output
--units	the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol
-v	Verbose output