Dear Dr Sindhikara,
Thank you very much for your clarifying answer. Thanks a lot once again Sir.
On Thu, Jul 21, 2011 at 6:55 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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.
> --Dan
>
> On Thu, Jul 21, 2011 at 5:17 AM, Rajeswari A.
> <rajeswari.biotech.gmail.com>wrote:
>
> > 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
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>
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Received on Fri Jul 22 2011 - 00:00:03 PDT
