[gmx-users] How to concatenate tpr files?

Erik Marklund erik.marklund at kemi.uu.se
Tue Jan 24 09:06:15 CET 2017

Dear Leila,

The RMSD is, by default, calculated with respect to the coordinates in the tpr file, which is why you get different results with different tprs. Which one to choose depends on exactly what you want to measure.

Kind regards,

Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 23 Jan 2017, at 17:10, leila karami <karami.leila1 at gmail.com<mailto:karami.leila1 at gmail.com>> wrote:

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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