<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Date: Wed, 11 Apr 2012 08:38:05 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] g_wham problem with negative COM differences<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F857B2D.3050100@vt.edu" target="_blank">4F857B2D.3050100@vt.edu</a>><br>
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Anni Kauko wrote:<br>
> Hi!<br>
><br>
> I try to perform pmf calculations for case where a peptide shifts<br>
> through the membrane. My COM differences should vary from 2.3 to -2.5.<br>
><br>
> My problem is that g_wham plots negative COM difference as they would be<br>
> positive. In pullx-files the COM differences are treated correctly<br>
> (look below). My peptide is not symmetric, so profile curves are not<br>
> symmetric, so loosing the sign for COM difference screws my profile<br>
> curve completely.<br>
><br>
> I did not manage to find any pre-existing answers to this problem from<br>
> internet.<br>
><br>
> First datalines from pullx files:<br>
> (sorry for strange file names...)<br>
><br>
> pull_umbr_0.xvg:<br>
> 0.0000 6.26031 2.27369<br>
><br>
> pullz_umbr_23.xvg:<br>
> 0.0000 6.09702 0.0233141<br>
><br>
> pullz_umbr_50.xvg:<br>
> 0.0000 6.02097 -2.50088<br>
><br>
> g_wham command:<br>
> g_wham -b 5000 -it tpr_files.dat -ix pullz_files.dat -o<br>
> profile_test.xvg -hist histo_test.xvg -unit kCal<br>
><br>
> My pull code:<br>
><br>
> pull = umbrella<br>
> pull_geometry = distance<br>
> pull_dim = N N Y<br>
> pull_start = yes<br>
> pull_ngroups = 1<br>
> pull_group0 = POPC_POPS ; reference group is bilayer<br>
> pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled<br>
> pull_init1 = 0<br>
> pull_rate1 = 0.0<br>
> pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>
><br>
<br>
Your problem stems from the use of "distance" geometry. This method assumes the<br>
sign along the reaction coordinate does not change, i.e. always positive or<br>
always negative. If the sign changes, this simple method fails. You should be<br>
using something like "position" to allow for a vector to be specified. Perhaps<br>
you can reconstruct the PMF by separately analyzing the positive restraint<br>
distances and negative restraint distances (note here that "distance" really<br>
refers to a vector quantity, and thus it can have a sign), or otherwise create<br>
new .tpr files using "position" geometry, though I don't know if g_wham will<br>
accept them or not.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<span><font color="#888888"><br>
</font></span></blockquote></div><br>Thank's!<br><br>I managed to solve my g_wham problem by doing two things:<br><br>1. New tpr-files with proper pull code for g_wham.<br>2. I also needed to modify signs of pullf values: If value for pullx distance was negative, I reversed the sign of corresponding pullf value. I did that by my own script.<br>
<br>The new pull code:<br><br>; Pull code<br>
<br>pull = umbrella<br>pull_geometry = direction<br>pull_vec1 = 0 0 1<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = POPC_POPS ; reference group is bilayer<br>pull_group1 = C-alpha_&_r_92-94 ; group that is actually pulled<br>
pull_init1 = 0<br>pull_rate1 = 0.0<br>pull_k1 = 1000 ; kJ mol^-1 nm^-2<br> <br>I am little bit confuced, why I needed to tweak signes of pullf values. But like that I got the curve that resembles two half curve made for positive and negative pullx distances separately. That curve also makes sense from biochemical point of view. <br>
<br>-Anni<br><br>PS. Thank's for your excellent tutorials. They have been indispensable help for me to get started with gromacs!<br><br>-- <br>************************************************<br>
Anni Kauko, Ph.D.<br>Post Doctoral Researcher<br><br>Structural Bioinformatics Laboratory<br>Dept. of Biosciences, Biochemistry<br>Åbo Akademi University<br>
20520 Turku, Finland<br>phone: <a href="tel:%2B358%20%280%292%20215%204006" value="+35822154006" target="_blank">+358 (0)2 215 4006</a><br>mobile: <a href="tel:%2B358%20%280%2950-576%208656" value="+358505768656" target="_blank">+358 (0)50-576 8656</a><br>
<br>************************************************<br>