[gmx-users] g_wham gets stuck
amarcovitz at gmail.com
Thu Apr 29 15:41:10 CEST 2010
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
i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler.
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
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
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?
2) suppose that my histograms overlap is poor for some locations along the
pulling vector, how one can solve that?
3) To generate the input configurations - what is the ideal pulling
procedure? ( i used pull = constant_force, with a small value of K1)
Again, Thanks a lot for the quick reply
On Thu, Apr 29, 2010 at 10:33 AM, Jochen Hub <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.
>> 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,
> 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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