Re: AMBER: equilibration of peptide

From: David A. Case <>
Date: Sat, 22 Mar 2008 10:51:47 -0700

On Sat, Mar 22, 2008, tushar garud wrote:

> I am studying dynamics of a peptide which is of 32 amino acid.
> I minimized, heated and equilibrated it with implicit solvent(igb=2) and
> shake on (ntc=ntf=2).
> Graph of total energy after equilibration was deviating between -100 to
> -300. Can I say it has been equilibrated?

You can't say anything based just on the evidence you provide. For one thing,
the details of the thermostat affect energy fluctuations. Further, we don't
know anything about this peptide, or what the starting or final configurations
were. If it is not a folded and stable peptide, then you would need to use
specialized techniques (such as replica exchange) that are far beyond what
someone new to amber should probably try.

My general advice for people new to simulations is to study a published
simulation that does close to what you want, and see if you can understand how
to do the same (or a similar) calculation.


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Received on Fri Apr 18 2008 - 21:13:11 PDT
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