[gmx-users] Regarding getting trajectories in gromacs..

Dilip H N cy16f01.dilip at nitk.edu.in
Tue Apr 4 06:48:29 CEST 2017

I have ran a md simulation for
nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns)
dt = 0.002 ; 1e+07 fs
nstxout    = 5000 ; save coordinates every 20.0 ps
nstvout    = 5000 ; save velocities every 20.0 ps
nstenergy    = 5000 ; save energies every 20.0 ps
nstlog    = 5000 ; update log file every 20.0 ps
nstxout-compressed  = 5000      ; save compressed coordinates every 20.0 ps

ie., for 10 ns.. and when i view the trr file in vmd , the bonds are
stretched/compressed.. so i tried with the command
gmx trjconv -f md.trr/xtc -s md.tpr -pbc mol -o md-mol.xtc
this above command is for the whole 0 - 10 ns trajectory i got and all the
bonds are intact now..
My question is that if i want to get the trajectories for 0-2ns,
2-4ns,4-6ns,6-8ns, 8-10ns, ie for every 2ns ..how to get it..??
gmx trjconv -f md.trr -s md.tpr -o  new.gro -b 0 -e 200
with this command i got the gro file... but how to view the trajectory of
this file...

1] What are the commands that i need to give to view individual
trajectories of 2 ns intervals
2] and how to view those obtained trajectories of 2ns in vmd without
getting bonds stretched/elongated..

With Best Regards,

Ph.D Student

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