Hi Jochen, Seems as if this error was associated with the mpi version. Everything worked ok when running it locally.
Best regards / Magnus On Aug 12, 2013, at 1:50 PM, Jochen Hub <j...@gwdg.de> wrote: > Hi Magnus, > > I just read your mail. Sound very much like a bug, which never occurred > to me though. But I did not use -bs-method traj-gauss a lot. Does the > error also occur with -bs-method traj? > > Btw: with -bs-method traj-gauss or traj, you need realistic estimates of > the autocorrelation times (ACTs). If you underestimate the ACTs, you > will underestimate your errors. > > If this error still occurs with the latest version, could you make a > tar-ball of your tpr and pullf files, put them online, and send me the link? > > Then I will try to fix the bug. > > Best, > Jochen > > > Am 8/5/13 8:29 AM, schrieb Magnus Andersson: >> Hi, >> >> I have a problem with the error analysis of g_wham. The PMF profile and >> sampling windows looks good, but when I try to generate error bars g_wham >> hangs. This is what I do: >> >> g_wham_mpi -if pullf-files.dat -it tpr-files.dat -o -hist -nBootstrap 50 >> -bins 50 -bs-method traj-gauss -bsres -ac yes -bsprof -vbs >> >> This is the output after which it just hangs: >> >> Estimating integrated autocorreltion times ... [100%] ... done >> >> Back Off! I just backed up iact.xvg to ./#iact.xvg.4# >> Wrote iact.xvg >> win 0, aver = 3.413503 sig = 0.091051 >> win 1, aver = 3.440995 sig = 0.060213 >> win 2, aver = 3.536864 sig = 0.069048 >> win 3, aver = 3.462364 sig = 0.041276 >> win 4, aver = 3.508488 sig = 0.041967 >> win 5, aver = 3.474703 sig = 0.038848 >> win 6, aver = 3.546181 sig = 0.042018 >> win 7, aver = 3.558158 sig = 0.047886 >> win 8, aver = 3.870348 sig = 0.053350 >> win 9, aver = 3.895024 sig = 0.047226 >> win 10, aver = 3.905363 sig = 0.039718 >> win 11, aver = 3.989860 sig = 0.048854 >> win 12, aver = 4.033406 sig = 0.045494 >> win 13, aver = 4.077549 sig = 0.042215 >> win 14, aver = 4.096139 sig = 0.036315 >> win 15, aver = 4.174044 sig = 0.040574 >> win 16, aver = 4.119622 sig = 0.052487 >> win 17, aver = 4.177672 sig = 0.036798 >> win 18, aver = 4.148724 sig = 0.033967 >> win 19, aver = 4.228320 sig = 0.039398 >> win 20, aver = 4.161365 sig = 0.039424 >> win 21, aver = 4.176532 sig = 0.041844 >> win 22, aver = 4.224519 sig = 0.030001 >> win 23, aver = 4.468429 sig = 0.046136 >> win 24, aver = 4.536401 sig = 0.049635 >> win 25, aver = 4.666026 sig = 0.054179 >> win 26, aver = 4.670022 sig = 0.045487 >> win 27, aver = 4.866098 sig = 0.046887 >> win 28, aver = 4.935376 sig = 0.050013 >> win 29, aver = 4.891905 sig = 0.042927 >> Getting initial potential by integration. >> Initialized rapid wham stuff (contrib tolerance 3.33333e-08) >> Evaluating only 474 of 1500 expressions. >> >> 1) Maximum change 2.849816e-01 >> 100) Maximum change 2.216439e-03 >> 200) Maximum change 1.866839e-03 >> 300) Maximum change 1.612522e-03 >> 400) Maximum change 1.419577e-03 >> 500) Maximum change 1.266497e-03 >> 600) Maximum change 1.140793e-03 >> 700) Maximum change 1.034780e-03 >> 800) Maximum change 9.434951e-04 >> 900) Maximum change 8.635977e-04 >> 1000) Maximum change 7.927633e-04 >> 1100) Maximum change 7.293254e-04 >> 1200) Maximum change 6.720574e-04 >> 1300) Maximum change 6.200347e-04 >> 1400) Maximum change 5.725450e-04 >> 1500) Maximum change 5.290277e-04 >> 1600) Maximum change 4.890329e-04 >> 1700) Maximum change 4.521924e-04 >> 1800) Maximum change 4.181996e-04 >> 1900) Maximum change 3.867947e-04 >> 2000) Maximum change 3.577540e-04 >> 2100) Maximum change 3.308822e-04 >> 2200) Maximum change 3.060068e-04 >> 2300) Maximum change 2.829734e-04 >> 2400) Maximum change 2.616429e-04 >> 2500) Maximum change 2.418887e-04 >> 2600) Maximum change 2.235951e-04 >> 2700) Maximum change 2.066558e-04 >> 2800) Maximum change 1.909727e-04 >> 2900) Maximum change 1.764550e-04 >> 3000) Maximum change 1.630186e-04 >> 3100) Maximum change 1.505854e-04 >> 3200) Maximum change 1.390827e-04 >> 3300) Maximum change 1.284431e-04 >> 3400) Maximum change 1.186038e-04 >> 3500) Maximum change 1.095063e-04 >> 3600) Maximum change 1.010962e-04 >> 3700) Maximum change 9.332302e-05 >> 3800) Maximum change 8.613974e-05 >> 3900) Maximum change 7.950267e-05 >> 4000) Maximum change 7.337121e-05 >> 4100) Maximum change 6.770765e-05 >> 4200) Maximum change 6.247700e-05 >> 4300) Maximum change 5.764678e-05 >> 4400) Maximum change 5.318686e-05 >> 4500) Maximum change 4.906931e-05 >> 4600) Maximum change 4.526823e-05 >> 4700) Maximum change 4.175964e-05 >> 4800) Maximum change 3.852131e-05 >> 4900) Maximum change 3.553267e-05 >> 5000) Maximum change 3.277469e-05 >> 5100) Maximum change 3.022973e-05 >> 5200) Maximum change 2.788151e-05 >> 5300) Maximum change 2.571494e-05 >> 5400) Maximum change 2.371608e-05 >> 5500) Maximum change 2.187205e-05 >> 5600) Maximum change 2.017093e-05 >> 5700) Maximum change 1.860172e-05 >> 5800) Maximum change 1.715425e-05 >> 5900) Maximum change 1.581912e-05 >> 6000) Maximum change 1.458767e-05 >> 6100) Maximum change 1.345187e-05 >> 6200) Maximum change 1.240432e-05 >> 6300) Maximum change 1.143820e-05 >> 6400) Maximum change 1.054720e-05 >> 6500) Maximum change 9.725497e-06 >> 6600) Maximum change 8.967716e-06 >> 6700) Maximum change 8.268901e-06 >> 6800) Maximum change 7.624473e-06 >> 6900) Maximum change 7.030212e-06 >> 7000) Maximum change 6.482219e-06 >> 7100) Maximum change 5.976900e-06 >> 7200) Maximum change 5.510938e-06 >> 7300) Maximum change 5.081272e-06 >> 7400) Maximum change 4.685081e-06 >> 7500) Maximum change 4.319759e-06 >> 7600) Maximum change 3.982905e-06 >> 7700) Maximum change 3.672303e-06 >> 7800) Maximum change 3.385910e-06 >> 7900) Maximum change 3.121841e-06 >> 8000) Maximum change 2.878356e-06 >> 8100) Maximum change 2.653854e-06 >> 8200) Maximum change 2.446856e-06 >> 8300) Maximum change 2.255997e-06 >> 8400) Maximum change 2.080021e-06 >> 8500) Maximum change 1.917767e-06 >> 8600) Maximum change 1.768166e-06 >> 8700) Maximum change 1.630232e-06 >> 8800) Maximum change 1.503056e-06 >> 8900) Maximum change 1.385799e-06 >> 9000) Maximum change 1.277687e-06 >> 9100) Maximum change 1.178008e-06 >> 9200) Maximum change 1.086104e-06 >> 9300) Maximum change 1.001369e-06 >> Switched to exact iteration in iteration 9302 >> Converged in 9303 iterations. Final maximum change 9.98417e-07 >> >> Back Off! I just backed up profile.xvg to ./#profile.xvg.8# >> Wrote profile.xvg >> >> Any idea of what goes wrong? >> >> Best regards / >> >> Magnus >> > > -- > --------------------------------------------------- > Dr. Jochen Hub > Computational Molecular Biophysics Group > Institute for Microbiology and Genetics > Georg-August-University of Göttingen > Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. > Phone: +49-551-39-14189 > http://cmb.bio.uni-goettingen.de/ > --------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
