[gmx-users] PMF curve

Vijayaraj vijayaraj81 at gmail.com
Tue Nov 22 11:29:18 CET 2011


I have done umbrella sampling for 10ns on 23 windows and g_wham program
shows converged histograms and PMF curve. I used the following g_wham

g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -o profile.xvg
-hist histo.xvg -b 1000 -e 10000

I considered first 1ns simulation as equilibration. when I change the -b
from 1000 to 1500, 2000... I can still get converged PMF curve but the PMF
convergence is achieved at different places, for eg, when I increase -b the
PMF converges at -18, -17, -16. and g_wham do not show any warning for poor
sampling. Is there any problem with the sampling windows when I increase
the -b? or simply we can select the PMF curve as obtained wtih "-b 1000"?

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