[gmx-users] g_wham gets stuck

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 29 15:45:05 CEST 2010

Amir Marcovitz wrote:
> Thanks for your answers,
> I tried to struggle a bit more with that today.
> my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and 
> pullx-files.dat) are fine and consistent with other in terms of file 
> numbering. 
> i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.

Time and time again, we have to point out the bold warning on the Downloads page:

"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These 
compilers come with recent Linux distrubutions like Fedora 5/6 etc."

Buggy behavior that is difficult to diagnose is often due to these faulty compilers.

> i run: *g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal 
> -b 1000    *(my data is 16ns long and i ignore the first ns)
> and it starts reporting that the file are read:
> Reading file topol742.tpr, VERSION 4.0.5 (single precision)
> File topol742.tpr, 1 groups, geometry "distance", dimensions [N Y N], (1 
> dimensions)
>         grp 0) k = 1000.000  inittial distance = 2.41331
> Reading file topol748.tpr, VERSION 4.0.5 (single precision)
> Reading file topol761.tpr, VERSION 4.0.5 (single precision)
> Reading file topol792.tpr, VERSION 4.0.5 (single precision)
> and so on..
> it reports that the boundaries are found and continue to read until it 
> stucks..
> However, when i do the WHAM with the pullx files (i.e., -ix pullx-files 
> instead of -if pullf-files.dat) the wham converges within a reasonable 
> time to a PMF profile which not so smooth.
> i therefore have some questions:
> 1) what is the difference in the profiles for using  pullx or pullf files?

In principle, there probably shouldn't be any, but if there is perhaps someone 
else has seen that.

> 2) suppose that my histograms overlap is poor for some locations along 
> the pulling vector, how one can solve that?

Better sampling (more time) within the sampling windows, or more closely-spaced 

> 3) To generate the input configurations -  what is the ideal pulling 
> procedure?  ( i used     pull = constant_force, with a small value of K1)

There isn't one "best" method, per se.  The only criterion is that you have 
generated configurations from which you can derive reasonably-spaced windows in 
which you do sufficient sampling.


> Again, Thanks a lot for the quick reply
> Amir
> On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub <jochen at xray.bmc.uu.se 
> <mailto:jochen at xray.bmc.uu.se>> wrote:
>     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.
>     Jochen
>         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
>     ---------------------------------------------------
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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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