[gmx-users] Extract frames from Trajectory

Harsha Ravishankar hara0050 at gapps.umu.se
Tue Nov 27 16:15:42 CET 2018


I need to extract frames from a 100 ns membrane protein simulation
trajectory which contains the protein molecule and lipid molecules which
are at a distance of 0.2 nm from its transmembrane domain.

First, I made an index file containing the residues of the transmembrane
domain named residues.ndx,

Then i made use of gmx select to identify the lipid molecules which are 0.2
nm away from them in the trajectory,

gmx select -f Traj.trr  -s topol.tpr -select 'resname POPC and within 0.2
of group 30' -n residues.ndx  -on Lipids.ndx,

Here I get an index file containing indices of individual atoms, which I
would like to use to extract frames of the protein + lipid molecules from
the simulation trajectory, but i am not sure how to.

Any help would be appreciated,



Harsha Ravishankar
Doctoral Candidate
Department of Chemistry
Umeå University, Umeå, Sweden

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