Dear Amber users/developers,
I am running Langevin dynamics simulations (ntt=3) for organic solvent
using Amber 11, and would like to calculate the self-diffusion coefficient
from the MSD vs. tau plot. My input file has inwrap=0 (default). I wonder
if I can use this trajectory to calculate MSD vs. tau directly? Or do I
need to post-process the trajectory by wrapping and re-centering the
primary box, and then unwrapping it, before the MSD calculation? In another
word, I was wondering if AMBER removes center of mass motions automatically
during simulation? Thank you very much in advance!
Best,
Mo
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Received on Tue Sep 18 2012 - 12:30:02 PDT
