[gmx-users] Extract frames from Trajectory

Justin Lemkul jalemkul at vt.edu
Tue Nov 27 16:40:36 CET 2018

On 11/27/18 10:24 AM, Fernando Nunes wrote:
> Try use -dump option and put exact time of the frame you want.

The trjconv -dump option requires manual selection of which frames to 
write, which could be quite cumbersome here.

An alternate approach is to generate a time series with some values that 
indicate that the criterion is satisfied, either a boolean operator (1 
or 0) that indicates the lipid is within range, or use a minimum 
distance criterion to indicate whether a lipid is close to the protein. 
Then, one can use trjconv -drop to read that .xvg file and 
-dropover/-dropunder to automatically select the frames of interest.


> 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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Justin A. Lemkul, Ph.D.
Assistant Professor
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