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

Mark Abraham mark.j.abraham at gmail.com
Sat Dec 3 00:07:52 CET 2016


There are some other ways to subsample trajectory files, check out the help
text. IIRC you can give it an index file of frame numbers, or something
like that.


On Fri, 2 Dec 2016 23:01 Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
> 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?
> Best,
> Irem
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