Re: Reg: movement of protein outside box

From: Aron Broom (
Date: Mon Jun 09 2014 - 22:09:28 CDT

you should do a search on this protein moving outside the box, I'm certain
that question has been raised many times.

In terms of equilibration and production, production simply suggests it's
the stuff you are actually going to analyze.

When you initially setup the system there are a usually things about those
initial coordinates that are not favourable. For instance, the water will
generally just be a large box where any waters clashing with your protein
are removed, this means that the interface of the water with your protein
isn't optimal, and there will need to be some movement and reorientation.
 There are other properties like that, but the point being, the type of
dynamics doesn't really define equilibration vs. production, equilibration
is just some initial simulation time where you expect the state of the
simulation may be "rapidly" changing to reach some energy minimum (which
you often hope is the global minimum, or at least the most relevant local

So you run until, for instance, the potential energy stops dropping, or the
RMSD of your protein stops changing, and then you ignore everything before
that and only analyze what comes after. Typically, numbers like 10 ns are
used for equilibration, but really, the judgement should be based on
factors like those measures mentioned above (many others could be used
also) and not just some arbitrary length of time.

On Mon, Jun 9, 2014 at 9:46 PM, Akshay Bhatnagar <> wrote:

> Hello everyone
> I have performed a 10 ns equilibration to simulate a amino acid in a 30 A
> water box, but after the equilibration the amino acid has moved to the
> corner of the box. can anyone explain me the reason?
> Also can anyone tell me the exact difference between equilibration and
> production run? If I use pressure control parameter in equilibration then
> is it equivalent to production run?
> Thank you very much
> With Regards
> Akshay Bhatnagar
> PhD Student
> BITS Pilani Hyderabad Campus

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

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