[gmx-users] trjconv_snapshot

rama david ramadavidgroup at gmail.com
Thu May 24 14:56:01 CEST 2012

On Thu, May 24, 2012 at 5:24 PM, Turgay Cakmak <turgaycakmak34 at gmail.com>wrote:

> Hi Gromacs users,
> I have a problem getting a snapshots using trjconv. If you could help me,
> I would be very grateful. Below, I try to explain what I did and problem
> happened.
> Firstly, I have done 10ns long simulation (several peptides in a box). And
> then, using the outputs of that simulation (conf10ns.gro and 10ns.cpt
> files), I extend the simulation 10 ns more and I get conf20ns.gro,
> trj20ns.xtc,….
> Then I used the following to get snapshot of the last frame.
> trjconv –f traj20ns.xtc –s topol.tpr –b 10000 –e 10000 –o
> snapshot20ns.gro      (Note: traj20ns.xtc is not a full trajectory, it
> just a trajectory of second 10ns simulation)
> When I looked these two files (conf20ns.gro and snapshot20ns.gro) at the
> VMD, they were completely different configurations. As far as I know, the
> last frame is written in conf20ns.gro. So they must be the same. What is
> wrong here?
> By the way, I defined dt=0,002, nstxout=1000 and nsteps=5000000 in my mdp
> file.
> Thanks in advance,
> Turgay

Catenate two trajectory with help of trjcat -h

to get snapshot of particular time use trjconv -dump <time>
use appropriate pbc option

you are using -b 10000 -e 10000

means the snapshot at 10 ns
So I think conf20.gro is snapshot at 20 ns  so they may differ ...

With Best Wishes,
Rama David
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