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, Steven
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