Re: [AMBER] REMD doubt : how to know the protein is not trapped in a conformation

From: Daniel Sindhikara <>
Date: Thu, 21 Jul 2011 07:25:12 -0600

It's no simple problem, but if your system moves into one state and never
out, it is not in equilibrium. You should see switching between
conformations (or along some reaction coordinate) many times. Of course,
this all assumes you picked a good reaction coordinate or definition for
different conformation. So it may be the case that your temperature range
doesn't go high enough; there also, of course, could be other problems.
Hope this helps.

On Thu, Jul 21, 2011 at 5:17 AM, Rajeswari A.

> Dear amber users,
> Please help me to come out of the barrier of doubts!!!.
> I am doing replica exchange simulation of a protein in Explicit solvent.
> Started with one conformation (conformation-1) of a protein i ended up with
> another conformation (conformation-2) in almost all replica. My temperature
> swapping is even from the start to end.
> 1) My problem is, i am getting conformation-2 existing for
> longer timescale even when the replica is swapping from lower to higher and
> vice versa. Is it because of the stability of that particular conformation
> or is it trapped in that particular conformation? (but the exchange and
> swapping to all temperature space is even through out the simulation).
> 2) How to identify that my simulation has reached
> conformational equilibrium for calculating the thermodynamic properties.
> Can
> somebody explain me it in simple terms.
> Please help me.
> Rajeswari A
> Ph.D Research scholar,
> Computational Biophysics Lab,
> IIT Madras,
> India.
> _______________________________________________
> AMBER mailing list

Dr. Daniel J. Sindhikara
Institute for Molecular Science
AMBER mailing list
Received on Thu Jul 21 2011 - 06:30:03 PDT
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