[gmx-users] Trajectory

Steven Neumann s.neumann08 at gmail.com
Mon Jan 30 10:43:32 CET 2012

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

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,

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