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

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Thu, 21 Jul 2011 16:47:02 +0530

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,
AMBER mailing list
Received on Thu Jul 21 2011 - 04:30:02 PDT
Custom Search