[gmx-users] Trajectory

[Mark Abraham]

On 30/01/2012 8:43 PM, Steven Neumann 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
>

... iff the simulation completed successfully.

> I used trjconv -f md.trr -o mdnojump.xtc -pbc nojump
>
> 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)
>

Your choice of trjconv workflow demands that the protein be allowed to 
diffuse away. What VMD makes of that is not really of consequence to 
discuss here. Perhaps you can design a better trjconv workflow, as here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

> Can you please advise? I think I have to many frames in my trajectory, 
> how can I reduce it in trjconv?
>

trjconv -h

Mark
>
> Thank you,
>
> Steven
>
>
>

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