[gmx-users] Extract frames from Trajectory

[Fernando Nunes]

Try use -dump option and put exact time of the frame you want.

Harsha Ravishankar <hara0050 at gapps.umu.se> escreveu no dia terça,
27/11/2018 à(s) 15:16:

> Hi,
>
> 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,
>
> Thanks
>
> Harsha
>
>
>
> --
> Harsha Ravishankar
> Doctoral Candidate
> Department of Chemistry
> Umeå University, Umeå, Sweden
> --
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