[gmx-users] end-to-end distance

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 18 19:28:57 CET 2010

Zuzana Benkova wrote:
> 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.

g_dist should only be measuring the COM distance between the two selected 
groups, so I don't know what you mean by "combined all pairs" - perhaps you can 
provide an example (index groups, relevant output, what you were expecting, and 
why you think it's wrong)?  If your groups contain all starting residues in one, 
then all ending residues in another, then yes, you're going to get weird 
results.  If you have one chain that is residues 1-100, you should have a group 
for r_1 and a group for r_100; select those for g_dist analysis.  If another 
chain is residue 101-200, r_101 and r_200 are what you want, etc.

> 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.

It certainly should be possible to iteratively use g_dist to measure distances 
between whatever groups you select.  Fairly straightforward, actually, so if 
you're not getting what you expect, provide the information I asked for above 
and hopefully someone should be able to figure out what's going wrong.


> Zuzana Benkova


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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