[gmx-users] how to generate average structure from trajectory

[Justin Lemkul]

On 3/6/20 3:21 PM, Sadaf Rani wrote:
> Dear Subhomoi
> Thanks for your reply.
> I was doing the following:-
> discarding 1 ns trajectory by the following command:-
> gmx trjconv -f md.xtc -s md.gro -n index.ndx -b 1000 -e 2000 -o
> md_1000ps.xtc

If your simulation is longer than 2 ns, you are not just discarding the 
first 1 ns, you're also discarding everything after 2 ns by doing this.

> Extracting average structure by the following command:-
>
> gmx rmsf -s md.tpr -f md_1000ps.xtc  -o rmsf1000ps.xvg -ox
> average1000ps.pdb  -res -n index.ndx
> I am confused between using gmx rmsf and gmx cluster for getting average
> structure
>
> for clustering should I do the following?
> gmx cluster -f md_1000ps.xtc -s md.tpr -n index.ndx -av average1000ps.pdb
>
> Can you please correct me.

gmx rmsf produces an average structure, which has no physical meaning.

gmx cluster gives you the central structures of the cluster, which are 
physically real (directly from the trajectory) and reflect the structure 
with the lowest RMSD relative to the cluster membership.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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