Both files hist.xvg and profile.xvg both are simultaneous output of this command. I did not run it twice, once to get profile.xvg and then to get hist.xvg as you uderstood.<br><br><div class="gmail_quote">On Thu, Aug 11, 2011 at 5:42 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;"><div class="im"><br>
<br>
shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I used following command<br>
g_wham_4.5.4 -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal<br>
Both profile.xvg and hist.xvg are created with this command using same pullf.xvg and .tpr files.<br>
</blockquote>
<br></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
shahid Nayeem<div class="im"><br>
<br>
On Thu, Aug 11, 2011 at 5:07 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>
<br>
I did some more sampling and sending you profile.xvg, histo.xvg.<br>
and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg.<br>
please tell my the difference in profile.xvg and hist.xvg. Both<br>
should be same but I get different curves here.<br>
<br>
<br>
I can't tell you the difference because you haven't shown how they<br>
were generated. My blind guess is that hist.xvg (a very confusing<br>
name for a PMF profile) was generated from data that have poor<br>
sampling in two regions. The contents of profile.xvg look normal.<br>
I don't know which of these curves corresponds to histo.xvg,<br>
because the histograms therein look fine.<br>
<br>
Please make sure to give full descriptions of these files. You've<br>
quote a message that is over a month old. I've replied to hundreds<br>
of messages since then and I do not remember the full context of our<br>
discussion.<br>
<br>
-Justin<br>
<br>
On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul<br>
<<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>><br></div><div><div></div><div class="h5">
<mailto:<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<br>
using your<br>
tutorial.Off course changing the pull_direction suitable<br>
for my<br>
protein but more or less following the same strategy. I<br>
am using<br>
gromacs_4.5.4 and g_wham utility. The profile.xvg file<br>
which I<br>
get is attached and it shows two dips in PE curve. Please<br>
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.<br>
Your<br>
histograms should confirm this.<br>
<br>
-Justin<br>
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