g_wham (1) - Linux Man Pages

g_wham: weighted histogram analysis after umbrella sampling

NAME

g_wham - weighted histogram analysis after umbrella sampling

VERSION 4.0.1

SYNOPSIS

g_wham -o profile.xvg -hist histo.xvg -[no]h -nice int -[no]w -[no]xvgr -min real -max real -bins int -[no]prof -temp real -[no]flip -tol real

DESCRIPTION

This is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files generated by mdrun using umbrella sampling tocreate a potential of mean force (PMF). The options are

-o name of the PMF output file

-hist name of the histograms output file

-min minimum coordinate to use

-max maximum coordinate to use

Note: the program will throw out any data that is outside of min - max. The program will output the true min and max after completion, so you can use these values the next time. or you can use:

-noprof only calculate min and max

-bins number of bins to use in calculation

FILES

-o profile.xvg Output
 xvgr/xmgr file 

-hist histo.xvg Output
 xvgr/xmgr file 

OTHER OPTIONS

-[no]hno
 Print help info and quit

-nice int 0
 Set the nicelevel

-[no]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-min real 0
 Minimum coordinate in profile

-max real 0
 Maximum coordinate in profile

-bins int 100
 Number of bins in profile

-[no]profyes
 Only calculate min and max

-temp real 298
 Temperature

-[no]flipno
 Combine halves of profile

-tol real 0.01
 Tolerance

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.