Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal -histo. But now as suggested by you I added -b 1000 -e 10000 leaving 1ns for equilibriation. The new profile.xvg is attached. How can I further improve it.<div>
<br></div><div>Shahid Nayeem<br><br><div class="gmail_quote">On Tue, Feb 21, 2012 at 1:04 AM, 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 am attaching a profile.xvg and histo.xvg. In each window 10ns sampling was done. The umbrella pullcode used is as follows.<br>
; Pull code<br>
pull = umbrella<br>
pull_geometry = distance ; simple distance increase pull_dim = Y N Y<br>
pull_vec1 = 0.75 0 1<br>
pull_start = yes ; define initial COM distance > 0<br>
pull_ngroups = 1<br>
pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns<br>
pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>
<br>
Please tell me my profile.xvg and histo.xvg are fine or not. In profile.xvg why i am not getting smooth convergence.<br>
</blockquote>
<br></div>
They're not terrible, but could be better. The PMF profile is a little rough and there are some regions of the reaction coordinate with little sampling. Maybe your simulations need to be longer and/or you need to exclude some amount of time at the beginning of each as equilibration (which you probably should do anyway, but without seeing your g_wham command, there's no way to know what you may or may not be considering).<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 Mon, Feb 20, 2012 at 8:24 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>
Thanks Justin<br>
I have pulled one of the chain from an initial COM distance<br>
value of 3.65 A to 7.90 A. When I look this trajectory in VMD I<br>
find that the<br>
<br>
<br>
I will have to assume you mean nm. Gromacs does not deal in<br>
Angstrom, and these distances would be within any sensible<br>
short-range cutoff and thus not indicative of actual separation.<br>
<br>
<br>
chain is completely separated. But even at this separation the<br>
profile.xvg file does not show its convergence to one value. I<br>
sent this file to you earlier.<br>
<br>
<br>
Sorry, I don't have a photographic memory, nor can I recall if<br>
you've ever posted your .mdp file, or at the very least, told us how<br>
much sampling you've done in each window. It may well be that your<br>
simulations are simply too short to observe adequate<br>
post-equilibration sampling.<br>
<br>
<br>
-Justin<br>
<br></div>
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Virginia Tech<br>
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