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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