On Wed, Jan 10, 2018, M. Pyrka wrote:
>
> I have problem with visualisation of trajectory of protein - ligand
> production in explicit solvent in VMD, namely during simulation ligand
> is suddenly going outside the binding site and after few hundreds steps
> it returns and stay there. It seems to be shifted to other picture by a
> vector. There is no rotation at the time when ligand is outside, which
> should occur for reliable simulation results. For these reasons I
> suppose this is a visualisation problem.
Try processing the trajectory file with cpptraj, and use the "autoimage"
option.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 10 2018 - 05:30:04 PST
