I used following command<div>g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal</div><div>Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files.</div><div>shahid Nayeem<br>
<br><div class="gmail_quote">On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Justin<div class="im"><br>
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.<br>
<br>
</div></blockquote>
<br>
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.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
shahid nayeem wrote:<br>
<br>
Dear Justin<br>
I did pmf calculation for my protein-protein complex using your<br>
tutorial.Off course changing the pull_direction suitable for my<br>
protein but more or less following the same strategy. I am using<br>
gromacs_4.5.4 and g_wham utility. The profile.xvg file which I<br>
get is attached and it shows two dips in PE curve. Please see it<br>
and tell me why I am getting these dips.<br>
<br>
<br>
You have insufficient sampling in at least these two regions. Your<br>
histograms should confirm this.<br>
<br>
-Justin<br>
<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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