Re: Re: Diffusion of Protein through the membrane

From: Cesar Luis Avila (
Date: Wed Jun 27 2007 - 08:12:00 CDT

To get rid of the diffusion why don't you just align the C alpha atoms
of your protein between frames before calculating the rmsd.
Ilya Chorny escribió:
> Hello All,
> 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 whole?
> Thanks,
> Ilya
> --
> Ilya Chorny Ph.D.

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