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?? ? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.