[gmx-users] How to concatenate tpr files?

leila karami karami.leila1 at gmail.com
Mon Jan 23 17:11:07 CET 2017

Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?


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