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

[spss4]

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


Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 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.di...@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
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[gmx-users] Regarding getting trajectories in gromacs..

[Dilip H N]

Hello,
I have ran a md simulation for
nsteps = 500 ; 2 * 500 = 1 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,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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