g_wham(1)
NAME
g_wham - weighted histogram analysis after umbrella sampling
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]h no
- Print help info and quit
- -nice int 0
- Set the nicelevel
- -[no]w no
- View output xvg, xpm, eps and pdb files
- -[no]xvgr yes
- 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]prof yes
- Only calculate min and max
- -temp real 298
- Temperature
- -[no]flip no
- Combine halves of profile
- -tol real 0.01
- Tolerance
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.