[gmx-users] Problem with the MDS extended trajectory in Gromacs 5.04

PAULAMI CHATTERJEE chatterjee_paulami at yahoo.co.in
Thu Jul 9 10:16:25 CEST 2015

Dear All,
I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I gave the following commands
gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr
gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append
After completion of the extension two new trajectory files were generated- 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the trajectory with
gmxcheck -f traj_comp.xtc
the output is
Checking file traj_comp.xtc
Reading frame 0 time 30000.000 
# Atoms 16867
Precision 0.001 (nm)
Last frame 35000 time 100000.000

This trajectory file contains coordinate values from 30ns to 100ns. I tried to calculate the rmsd with this file (both the trr and xtc file) but the graph abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the calculation I need the total trajectory from time 0 to time 100ns.I think I am missing something.
Can anyone please suggest anything here? Which one is the total trajectory file then?
Thanks in advancePaulami 

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