[gmx-users] trjconv_snapshot

Turgay Cakmak turgaycakmak34 at gmail.com
Thu May 24 13:54:30 CEST 2012

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
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,

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
Thanks in advance,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120524/ecb4459a/attachment.html>

More information about the gromacs.org_gmx-users mailing list