[gmx-users] trjconv sampling according to a list of arbitrary times

Irem Altan irem.altan at duke.edu
Sat Dec 3 00:00:56 CET 2016


I have a very long simulation and I want to run trjconv on the output to save snapshots from a list of times. For instance if t = [1,20, 220, 620] in ps, I would do:

gmx trjconv -f all.trr -s nvt.tpr -dump 1 -o conf1.pdb
gmx trjconv -f all.trr -s nvt.tpr -dump 20 -o conf2.pdb
gmx trjconv -f all.trr -s nvt.tpr -dump 220 -o conf3.pdb
gmx trjconv -f all.trr -s nvt.tpr -dump 620 -o conf4.pdb

and then join them with trjcat. This is very easy to do with a script. My problem is, each time I run trjconv, gromacs scans the .trr file from the first frame until the desired frame. So if I want to save 300 such configurations, I have to wait for the file to be read 300 times.

Is it possible to do this with a single trjconv command, and somehow provide a list of the times I want to sample, so that gromacs reads the file once and saves the necessary snapshots?


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