Mark.Abraham at anu.edu.au
Mon Jan 30 13:16:23 CET 2012
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
> Can you please advise? I think I have to many frames in my trajectory,
> how can I reduce it in trjconv?
> Thank you,
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