My system is a protein-protein complex. After pulling I selected windows at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and thereafter windows at 0.2nm spacing was selected upto 7.5nm. In each window 10ns MD was done and g_wham command was run neglecting the fist 1ns run for equilibriation.<div>
Shahid Nayeem <br><br><div class="gmail_quote">On Tue, Feb 21, 2012 at 6:42 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">
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.<br>
<br>
</blockquote>
<br></div>
I don't know. You've never even stated what your system is, how you decided on the window spacing or time in each window, etc. It may be that your simulations are too short. You have a few regions along the reaction coordinate that are not well-sampled, which could contribute to some rockiness in the PMF.<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><div></div><div class="h5"><br>
<br>
On Tue, Feb 21, 2012 at 1:04 AM, 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>
I am attaching a profile.xvg and histo.xvg. In each window 10ns<br>
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<br>
= 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<br>
profile.xvg why i am not getting smooth convergence.<br>
<br>
<br>
They're not terrible, but could be better. The PMF profile is a<br>
little rough and there are some regions of the reaction coordinate<br>
with little sampling. Maybe your simulations need to be longer<br>
and/or you need to exclude some amount of time at the beginning of<br>
each as equilibration (which you probably should do anyway, but<br>
without seeing your g_wham command, there's no way to know what you<br>
may or may not be considering).<br>
<br>
-Justin<br>
<br>
Shahid Nayeem<br>
<br>
<br>
On Mon, Feb 20, 2012 at 8:24 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 class="im">
<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>
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<br>
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<br>
separation the<br>
profile.xvg file does not show its convergence to one<br>
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<br>
us how<br>
much sampling you've done in each window. It may well be<br>
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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