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]>> 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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==============================__==========
Justin A. Lemkul
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Department of Biochemistry
Virginia Tech
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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