shahid nayeem wrote:
I used following command
g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
Both profile.xvg and hist.xvg are created with this command using same
pullf.xvg and .tpr files.
An identical command with identical input files producing totally different
output? Sorry, but I find that hard to believe. Check your work and make sure
you're using the input you think you are. I suspect something's amiss and
you're not seeing it.
-Justin
shahid Nayeem
On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
Dear Justin
I did some more sampling and sending you profile.xvg, histo.xvg.
and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg.
please tell my the difference in profile.xvg and hist.xvg. Both
should be same but I get different curves here.
I can't tell you the difference because you haven't shown how they
were generated. My blind guess is that hist.xvg (a very confusing
name for a PMF profile) was generated from data that have poor
sampling in two regions. The contents of profile.xvg look normal.
I don't know which of these curves corresponds to histo.xvg,
because the histograms therein look fine.
Please make sure to give full descriptions of these files. You've
quote a message that is over a month old. I've replied to hundreds
of messages since then and I do not remember the full context of our
discussion.
-Justin
On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
shahid nayeem wrote:
Dear Justin
I did pmf calculation for my protein-protein complex
using your
tutorial.Off course changing the pull_direction suitable
for my
protein but more or less following the same strategy. I
am using
gromacs_4.5.4 and g_wham utility. The profile.xvg file
which I
get is attached and it shows two dips in PE curve. Please
see it
and tell me why I am getting these dips.
You have insufficient sampling in at least these two regions.
Your
histograms should confirm this.
-Justin
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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ICTAS Doctoral Scholar
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
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