[gmx-users] g_wham gets stuck
Jochen Hub
jochen at xray.bmc.uu.se
Fri Apr 30 15:00:01 CEST 2010
Justin A. Lemkul wrote:
>
>
> 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.
It should not make any difference at all. It it does, there is something
wrong with the data or g_wham is buggy. With the pullf files, g_wham
simply computes the pullx values from the force and the force constant.
This is not really required since it is more natural to just work with
the pullx, but I added to for the case that someone forgot to write the
pullx and only has the pullf files.
>
>> 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 windows.
And maybe stronger force constants. g_wham can combine the runs with
smaller and larger force constants, that is no problem.
That is probably the reason for the weired PMF!
Jochen
>
>> 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.
>
> -Justin
>
>>
>> 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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>
--
---------------------------------------------------
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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