[gmx-users] end-to-end distance

Berk Hess gmx3 at hotmail.com
Thu Feb 18 20:22:12 CET 2010

Use g_polystat.


From: Zuzana.Benkova at savba.sk
To: gmx-users at gromacs.org
Date: Thu, 18 Feb 2010 19:20:10 +0100
Subject: [gmx-users] end-to-end distance

Dear GROMACS users, 

I have a system of 64 chains and want to calculate averaged values of end-to-end distance of all chains as well as the averaged radius of gyration from 1ns trajectory. In the case of end-to-end distance I have prepared index file containing one group of the first atoms in ascending order and the second one containing the terminal atoms in ascending order. I have used g_dist but it looks like it combined all pairs between both groups. I have looked at the mailing list but did not find the answer. 

Is it possible to do such analysis using directly GROMACS tools or I need to prepare some scripts with loops running over all chains. Thank you for response in advance.

Zuzana Benkova
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