[gmx-users] Trajectory

[lina]

On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> Dear Gmx Users,
>
> I run the simulation of protein with 10 ligands (200 ns). In total I should
> have total of 4000 frames as I set up:
>
> nsteps = 100000000
>
> dt = 0.002
>
> nstxout = 25000
>
> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump

-dt 4000

now you will only have 51 frames. more info. check trjconv -h

>
> The trajectory which I read in VMD has 3008 frames and my ligands completely
> disappear after 8 frame (They are not in PBC windows which I checked in
> Graphics -> Graphical Representation -> Periodic)
>
> Can you please advise? I think I have to many frames in my trajectory, how
> can I reduce it in trjconv?
>
> Thank you,
>
>
>
> Steven
>
>
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