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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>> 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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Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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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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