[gmx-users] g_wham error analysis hangs
Justin Lemkul
jalemkul at vt.edu
Mon Aug 5 13:46:25 CEST 2013
On 8/5/13 2:29 AM, Magnus Andersson wrote:
> 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?
>
I've had this happen before when trying to analyze too many data points. Try
reducing the size of the input data using -b to see if that helps.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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