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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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