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g_whamMain Table of Contents |
VERSION 3.3.1
Thu 11 May 2006
| VERSION 3.3.1 |
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
| option | filename | type | description |
|---|---|---|---|
| -o | profile.xvg | Output | xvgr/xmgr file |
| -hist | histo.xvg | Output | xvgr/xmgr file |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -nice | int | 0 | Set the nicelevel |
| -[no]w | bool | no | View output xvg, xpm, eps and pdb files |
| -[no]xvgr | bool | 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 | bool | yes | Only calculate min and max |
| -temp | real | 298 | Temperature |
| -[no]flip | bool | no | Combine halves of profile |
| -tol | real | 0.01 | Tolerance |