[gmx-users] g_wham gets stuck

Amir Marcovitz amarcovitz at gmail.com
Sun May 2 11:25:32 CEST 2010 

Thank you Jochem,

In your last reply, did you mean that i can perform the WHAM on Various
histograms that were collected with different force constants? i mean , will
it know to do the correction for the biasing potential
amir
On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub <jochen at xray.bmc.uu.se> wrote:

> 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
>>>    ---------------------------------------------------
>>>
>>>
>>>    --     gmx-users mailing list    gmx-users at gromacs.org
>>>    <mailto:gmx-users at gromacs.org>
>>>    http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>    Please search the archive at http://www.gromacs.org/search before
>>>    posting!
>>>    Please don't post (un)subscribe requests to the list. Use the www
>>>    interface or send it to gmx-users-request at gromacs.org
>>>    <mailto:gmx-users-request at gromacs.org>.
>>>    Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>
>
> --
> ---------------------------------------------------
> 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
> ---------------------------------------------------
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
>  http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100502/948118b7/attachment.html>

More information about the gromacs.org_gmx-users mailing list