[gmx-users] concatenate 2 trajectory files

Mark Abraham mark.j.abraham at gmail.com
Fri Jul 28 18:08:22 CEST 2017


On Fri, 28 Jul 2017 17:49 Atila Petrosian <atila.petrosian at gmail.com> wrote:

> Dear gromacs users,
> I had done a md simulation for 100 ns. I continued that for another 50 ns.
> gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx
> gmx mdrun -nb gpu -v -deffnm 100
> gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx
> gmx mdrun -nb gpu -v -deffnm 50
> I concatenated these 2 trajectories (100.xtc and 50.xtc) using
> gmx trjcat -f 100.xtc 50.xtc -o 150.xtc -settime

Seems like you should simply use

gmx mdrun -s 100
gmx convert-tpr -f 100 -o 150 -extend 50
gmx mdrun -s 150 -cpi

and let the automated appending work for you, rather than you fussing with
getting filenames and -settime right. The latter does not scale well.

I want to know for analysis on final trajectory (150.xtc), which of
> tpr files is appropriate (100.tpr or 50.tpr)?

Depends on your analysis. They differ only in the contained configuration,
and the number of steps, so you decide. Generally, it's irrelevant.

Should I concatenate
> tpr files?

What would that even mean?


> Atila
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