[gmx-users] g_wham gets stuck
Jochen Hub
jochen at xray.bmc.uu.se
Mon May 3 11:58:17 CEST 2010
Amir Marcovitz wrote:
> 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
Yes, WHAM does not require identical force constants. Just make sure
that the order of tpr and pullx files agree in the -it and -ix input agree.
Jochen
> amir
> On Fri, Apr 30, 2010 at 4:00 PM, Jochen Hub <jochen at xray.bmc.uu.se
> <mailto: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>
> <mailto: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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--
---------------------------------------------------
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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