From: Ilya Chorny (ichorny_at_gmail.com)
Date: Tue Jun 26 2007 - 22:12:22 CDT
After analyzing my trajectories of a large protein in a membrane, I noticed
the my protein shifts about 3 A after about 10 ns. Would one expect
diffusion on this time scale? Taking a diffusion constant of about 10^-8
cm^2/s the conversion into MD units is .1A^2/ns (if I did the math right),
thus 3 A seems a bit much. Any thoughts?
I am also working with a manic cluster which kills my jobs every so often,
at which point I restart the trajectories with new initial veloocites. Could
restarting with new initial velocities cause a shift/diffusion.
Finally, I do not zero the CM motion of the system. Does that mean I have a
non-zero CM velovity, and thus I should expect the system to drift as a
-- Ilya Chorny Ph.D.
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