[gmx-users] Merging of two trajectories

Justin Lemkul jalemkul at vt.edu
Wed Jul 18 13:40:12 CEST 2012

On 7/18/12 7:35 AM, James Starlight wrote:
> 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?

Use trjcat to concatenate the trajectories.  The -settime option will allow you 
to fix any potential issues with timestep, though if the simulations were all 
run with Gromacs and continued via .cpt file, there should be no need.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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