Re: Random seed and equilibrated structure

From: Aron Broom (
Date: Thu Jul 26 2012 - 16:07:32 CDT

I'm not sure if that would show you what you want. If your run has
stabilized, it suggests you are now in some kind of reasonably deep
minimum. Presumably you are thinking of doing multiple runs to make sure
that it is actually the deepest minimum near to your starting point, and if
so, randomizing the seed from your already equilibrated structure may end
up just telling you that you have high walls around that minimum, even if
there are other deeper minima nearby.

Also, in terms of using the RMSD a measure of the simulation stabilizing,
do you just plot the RMSD as compared to the first frame? That is
generally what I've done, but I wonder if others have different
approaches? The big problem with that is the ambiguity of the RMSD, that
is, if the RMSD levels off at 3A, it means that two structures in the last
part of your simulation are different from the starting structure by 3A,
but they could be more different than that from one another. I've tried
using VMD to do an RMSD versus lag time or something, which would be a kind
of fluctuation measure, and found that could be more sensitive. I'd like
to know what others do with this, maybe there is something obvious I've


On Thu, Jul 26, 2012 at 4:55 PM, Dr. Eddie <> wrote:

> Hi all,
> I've been simulating a protein with NAMD using constant pressure
> and temperature and PME. It takes anywhere from 10-24 ns for the rmsd of
> the protein's backbone to level-off. I'd like to have multiple runs to
> ensure good statistics but that overhead is debilitating. Would I be able
> to simply continue a run that has stabilized (after, say 30 ns) using
> different random seeds to get the same result as having multiple runs start
> with different random seeds and each running for 30+ ns?
> Has anyone tried this? I'd be interested in success or failure since my
> time scales are too long to try it myself.
> Thanks,
> Eddie

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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