[gmx-users] g_wham gets stuck

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 28 22:21:11 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..

For problems like these (which are hard to diagnose!), your Gromacs version, 
compilers used, OS, etc. would be useful.

> 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.
> i then run g_wham (with -it and -if) and it works fine at the beginning, 

A real command line would be better.  Does g_wham report reading in all of the 
files correctly?

> but then the computer simply gets stuck (!?) and the calculation is 
> killed -  with no error massage.
> what is it that I'm doing wrong?

Not a clue, based on what you've provided.  Sounds like a reasonable procedure 
to me.

> it looks like my output data (pullf and tpr files) are fine, but is it 
> possible that some of them causing the problem?

Are your input files (.dat) intact?  In the appropriate order, etc?  Are all 
your file names unique?  Additional details like these would be good.  You can 
also add the -debug flag to get a .log file of what g_wham is doing.  That might 
be useful.


> this is really frustrating..
> need your help,
> Amir


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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