[gmx-users] g_wham error analysis hangs
Jochen Hub
jhub at gwdg.de
Mon Aug 12 13:50:28 CEST 2013
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/
---------------------------------------------------
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