From: Ilya Chorny (ichorny_at_gmail.com)
Date: Wed Jun 27 2007 - 09:57:49 CDT
Peter,
Does it really matter if I assign new velocities when I restart a job? Some
thermostats work by reassigning the velocities every so often. I do use bin
coordinates to restart the job.
Thanks,
Ilya
On 6/27/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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
> simulation.
> Peter
>
> 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.
>
-- Ilya Chorny Ph.D.
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