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.
-Justin
Zuzana Benkova
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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