[gmx-users] Merging of two trajectories

James Starlight jmsstarlight at gmail.com
Wed Jul 18 13:35:15 CEST 2012

Dear Gromacs Users!

I have two trajectories  with removed PBC which was done by the below command.

trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc
mol -ur compact

Both of that trajectories are of the same system- when one trajectory
have been manyally stoped I've run the second one from the end of the
first trajectory using cpt file of the first simulation.

I have no problem with that data but when I try to merge it by means
of VMD and obtain the whole file I noticed that new trajectory consist
of wrong kinetik data.

E.g on the RMSD or some other graph the TIME values are always
incorrect. How I could prevent this and obtain correct whole
trajectory file from 2 or more parts?

Thanks for help


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