[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
> 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
> 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
> this is really frustrating..
> need your help,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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