[gmx-users] g_wham gets stuck

Jochen Hub jochen at xray.bmc.uu.se
Thu Apr 29 09:33:17 CEST 2010

Amir Marcovitz wrote:
> Hi All,
> I have some problems with g_wham, and i already gone through all the 
> postings and didn't find a hint..
> basically, I'm trying to calculate PMF between two charged plates. 
> I've performed a pulling simulation between the 2 plates according to 
> Justin's UMBRELLA tutorial in the website (all steps, i.e., 
> minimization, equilibration etc. up to that point work fine)
> from the pulling i generated input configurations for the umbrella 
> sampling runs (pull=umbrella , rate=0.0), which are 15 ns long
> and collected all the output pullf.xvg and *.tpr files.
You could also run g_wham -histonly to get the histogram file. Then 
check with xmgrace -nxy histo.xvg whether the histograms properly overlap.

But if they do not overlap, I would rather expect g_wham to give a zero 
PMF or to iterate forever, so not sure what is wrong.


> i then run g_wham (with -it and -if) and it works fine at the 
> beginning, but then the computer simply gets stuck (!?) and the 
> calculation is killed -  with no error massage.
> what is it that I'm doing wrong?
> it looks like my output data (pullf and tpr files) are fine, but is it 
> possible that some of them causing the problem?
> this is really frustrating..
> need your help,
> Amir

Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

More information about the gromacs.org_gmx-users mailing list