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g_wham_d
Langue: en
Version: 264976 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_wham - weighted histogram analysis after umbrella samplingSYNOPSIS
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 realDESCRIPTION
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 Outputxvgr/xmgr file
-hist histo.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]h noPrint 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
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
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