[gmx-users] Umbrella sampling tutorial WHAM issue
Justin Lemkul
jalemkul at vt.edu
Thu Nov 10 16:47:48 CET 2016
On 11/10/16 10:46 AM, Lindsay, Richard J. wrote:
> 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.
>
You're probably just plotting it wrong. xmgrace -nxy histo.xvg, not xmgrace
histo.xvg.
-Justin
> 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??
>
> ?
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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