[gmx-users] Umbrella sampling tutorial WHAM issue
Lindsay, Richard J.
lindsayrj at ornl.gov
Thu Nov 10 16:46:10 CET 2016
Hi,
I am attempting to follow the gromacs umbrella sampling tutorial but have run into an issue at the data analysis step.
When I run the gmx wham command I get only one histogram, even though I collected 24 umbrella trajectories.
Here is the command I am running:
gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
The *-files.dat files each contain a list of the 24 relevant files as such:
pullf-files.dat:
pullf-umbrella0.xvg
...
...
pullf-umbrella23.xvg
tpr-files.dat:
umbrella0.tpr
...
...
umbrella23.tpr
When I run the analysis on one .tpr/.xvg file at a time and run the analysis 24 times I am able to combine the histograms produced to get the expected result: 24 well-spaced histograms with reasonable overlap. However I would like to know why I am unable to get this result by running gmx wham once as in the tutorial. I am using gromacs 5.1.2.
Here is the log file from my original attempt at the wham analysis:
----------------------------------------------------------------------------------------------------------------------------------
Note: Will use 32 OpenMP threads.
Found 24 tpr and 24 pull force files in tpr-files.dat and pullf-files.dat, respectively
Reading 12 tpr and pullf files
Automatic determination of boundaries...
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 dimensions)
Pull group coordinates not expected in pullx files.
crd 0) k = 1000 position = 0.489812
Use option -v to see this output for all input tpr files
Reading pull force file with pull geometry distance and 1 pull dimensions
Expecting these columns in pull file:
0 reference columns for each individual pull coordinate
1 data columns for each pull coordinate
With 1 pull groups, expect 2 columns (including the time column)
Determined boundaries to 0.445155 and 5.253408
Wrote histo.xvg
Getting initial potential by integration.
Initialized rapid wham stuff (contrib tolerance 4.16667e-08)
Evaluating only 1013 of 4800 expressions.
1) Maximum change 5.820592e-01
100) Maximum change 6.205472e-03
200) Maximum change 1.677333e-03
300) Maximum change 1.011720e-03
400) Maximum change 6.767362e-04
500) Maximum change 5.057361e-04
600) Maximum change 3.887035e-04
700) Maximum change 3.053506e-04
800) Maximum change 2.443217e-04
900) Maximum change 1.986103e-04
1000) Maximum change 1.689707e-04
1100) Maximum change 1.467826e-04
1200) Maximum change 1.293663e-04
1300) Maximum change 1.141341e-04
1400) Maximum change 1.008461e-04
1500) Maximum change 8.925561e-05
1600) Maximum change 7.913347e-05
1700) Maximum change 7.036949e-05
1800) Maximum change 6.276724e-05
1900) Maximum change 5.603027e-05
2000) Maximum change 5.005392e-05
2100) Maximum change 4.474645e-05
2200) Maximum change 4.119858e-05
2300) Maximum change 3.794030e-05
2400) Maximum change 3.486749e-05
2500) Maximum change 3.199419e-05
2600) Maximum change 2.932535e-05
2700) Maximum change 2.685949e-05
2800) Maximum change 2.459074e-05
2900) Maximum change 2.251030e-05
3000) Maximum change 2.060762e-05
3100) Maximum change 1.887118e-05
3200) Maximum change 1.728904e-05
3300) Maximum change 1.584933e-05
3400) Maximum change 1.454045e-05
3500) Maximum change 1.335133e-05
3600) Maximum change 1.227147e-05
3700) Maximum change 1.129108e-05
3800) Maximum change 1.040106e-05
3900) Maximum change 9.593003e-06
4000) Maximum change 8.859203e-06
4100) Maximum change 8.192607e-06
4200) Maximum change 7.586786e-06
4300) Maximum change 7.035893e-06
4400) Maximum change 6.534625e-06
4500) Maximum change 6.078177e-06
4600) Maximum change 5.662203e-06
4700) Maximum change 5.282778e-06
4800) Maximum change 4.936358e-06
4900) Maximum change 4.619747e-06
5000) Maximum change 4.330065e-06
5100) Maximum change 4.064716e-06
5200) Maximum change 3.821363e-06
5300) Maximum change 3.597901e-06
5400) Maximum change 3.392435e-06
5500) Maximum change 3.203261e-06
5600) Maximum change 3.028843e-06
5700) Maximum change 2.867799e-06
5800) Maximum change 2.718886e-06
5900) Maximum change 2.580983e-06
6000) Maximum change 2.453083e-06
6100) Maximum change 2.334276e-06
6200) Maximum change 2.223746e-06
6300) Maximum change 2.120755e-06
6400) Maximum change 2.024637e-06
6500) Maximum change 1.934795e-06
6600) Maximum change 1.850688e-06
6700) Maximum change 1.771827e-06
6800) Maximum change 1.697773e-06
6900) Maximum change 1.628127e-06
7000) Maximum change 1.584411e-06
7100) Maximum change 1.549694e-06
7200) Maximum change 1.514711e-06
7300) Maximum change 1.479603e-06
7400) Maximum change 1.444496e-06
7500) Maximum change 1.409498e-06
7600) Maximum change 1.374703e-06
7700) Maximum change 1.340194e-06
7800) Maximum change 1.306039e-06
7900) Maximum change 1.272297e-06
8000) Maximum change 1.239020e-06
8100) Maximum change 1.206250e-06
8200) Maximum change 1.174022e-06
8300) Maximum change 1.142365e-06
8400) Maximum change 1.111303e-06
8500) Maximum change 1.080853e-06
8600) Maximum change 1.051032e-06
8700) Maximum change 1.021848e-06
Switched to exact iteration in iteration 8777
Converged in 8778 iterations. Final maximum change 9.99532e-07
Wrote profile.xvg
In case you use results from g_wham for a publication, please cite:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot and D. van der Spoel
g_wham - A free weighted histogram analysis implementation including robust
error and autocorrelation estimates
J. Chem. Theory Comput. 6 (2010) pp. 3713-3720
-------- -------- --- Thank You --- -------- --------
--------------------------------------------------------------------------------------------
Thanks,
Justin??
?
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