Thank you so much for your suggestion Dr. Case. The center command works well. Now my concern is if the center command affects the diffusion coefficient value of the system. Now I got a value that is 10 times smaller than the expected value. Is it more due to the force field? I used GAFF. Is there anyway to improve the self diffusion coefficient?
Thank you again
Best regards,
Quynh Vo
On Saturday, June 28, 2014 8:45 AM, David A Case <case.biomaps.rutgers.edu> wrote:
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 Tue Jul 01 2014 - 13:30:02 PDT
