[gmx-users] contact residues

Mark Abraham mark.abraham at anu.edu.au
Mon Aug 30 02:15:14 CEST 2010

----- Original Message -----
From: pawan raghav <pwnrghv at gmail.com>
Date: Friday, August 27, 2010 17:22
Subject: [gmx-users] contact residues
To: gmx-users at gromacs.org

> I have used g_mdmat
 g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg > 
> I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are in contact? how to get list of contact residues? 

That's not easy, unfortunately. GROMACS ought to be able to write an ASCII matrix of the .xpm data so that you can find out this kind of information, and while that's been on the to-do list for a while, I don't know if any progress has happened. In lieu, the best you can do is examine the axis scale and count suitably. Worst case, use trjconv to make a trajectory containing only a plausible subset of the residues, and examine the smaller matrix that g_mdmat will then produce.
> In graph file num.xvg there are three columns which I am not able to understand i.e. total, mean and natm. What is total, mean and natom

g_mdmat -h penultimate sentence of the description.


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