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

[spss4 at iacs.res.in]

  ----- Message from Dilip H N <cy16f01.dilip at nitk.edu.in> ---------
    Date: Tue, 4 Apr 2017 10:18:23 +0530
    From: Dilip H N <cy16f01.dilip at nitk.edu.in>
Reply-To: gmx-users at gromacs.org
Subject: [gmx-users] Regarding getting trajectories in gromacs..
      To: gromacs.org_gmx-users at maillist.sys.kth.se

> Hello,
> 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[1] -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,
>
> DILIP.H.N
> Ph.D Student
>
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----- End message from Dilip H N <cy16f01.dilip at nitk.edu.in> -----

Hi,
You can generate a .trr file using -b 0 -e 2000. Your command should be
gmx trjconv -s md.tpr -f md.trr -b 0 -e 2000 -o traj_0-2ns.trr -pbc mol
Then you just load it to VMD. You can see the 2 ns trajectory without bond
stretching. :)

Links:
------
[1] http://md.trr/xtc