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

[Daniel Adriano Silva M]

Hi,

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.

Daniel

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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