[gmx-users] How to find average protein structure.

Daniel Adriano Silva M dadriano at gmail.com
Fri Mar 4 07:35:25 CET 2011


I think g_covar can calculate the average structure (take a look to the
manual). However note that average structure could be a non relevant
structure, i.e. the average could represent an imposible conformation. So
maybe you can also give a try to g_cluster and look for the central
conformation. Good look.


2011/3/3 ajaniharesh at gmail.com <ajaniharesh at gmail.com>

> Hi everybody,
> I am new user of gromacs. I had run simulation for 1ns and have obtained
> all required output files. After comparing and analysing the potential
> energy and rms .
> Now i want to know how to find out the average protein structure between
> 1ps to 1000ps.
> Please help me.
> With regards.
> Sent from my Nokia phone
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