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 <joc...@xray.bmc.uu.se
<mailto:joc...@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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