On Thu, Jun 26, 2014, Quynh Vo wrote:
>
> I'm trying to calculate the self diffusion coefficient of a compound by
> simulating 500 molecules in a cubic box using NVE ensemble.
>
> When I visualized the simulation
> using VMD, the whole box drifted in one direction.
Try using the center command in cpptraj to center things, say on the first
solvent molecule. That should remove overall drift.
(I've not done this myself, so you may have to experiment.)
...dac
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Received on Sat Jun 28 2014 - 09:00:02 PDT
