Re: Re: Diffusion of Protein through the membrane

From: Peter Freddolino (
Date: Wed Jun 27 2007 - 08:51:04 CDT

When you have to restart a run, you should do so by using
binarycoordinates and binaryvelocities (set to the restart files from
your previous runs) and *not* assign new initial velocities. This may or
may not be responsible for what you saw (the COM motion may also be an
issue), but is certainly the only way to actually continue an existing

Ilya Chorny wrote:
> 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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