Since AMBER uses a velocity rescaling factor upon exchange, the replicas are
in equilibrium at the moment of exchange for NVT. To my knowledge, AMBER
does not do NPT exchanges. (Not sure if it is allowed or not). Most people
run relaxation simulations at NPT prior to REMD then freeze the volume for
NVT REMD simulation.
For information about rescaling see the original paper by Okamoto:
* Y. Sugita, Y. Okamoto, Chem. Phys. Lett. 314 (1999) 141. *
For information regarding frequency of exchanges (within NVT) see:
*D. Sindhikara, Y.L. Meng, A.E. Roitberg, J. Chem. Phys. 128 (2008) 24103.*
* *
*D.J. Sindhikara, D.J. Emerson, A.E. Roitberg, *J. Chem. Theory Comput.*. 6
(2010) 2804.*
Hope this helps!
--Dan
On Wed, May 11, 2011 at 8:19 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> Dear Amber users and developers,
>
> I am going to do some REMD calculations on a small peptide in a
> water molecules box and a question came up to me.
>
> When the first (and then the following ones) attempt to swap temperatures
> between two adjacent replica is successful, does not it creat instability
> in the
> two replica?
>
> I mean each of the replica involved has a new temperature and therefore is
> no
> longer at the equilibrium, what about the value of density (and
> pressure) at that
> temperature?
>
> If one is using an NPT ensemble, the replica are likely to `relax' and
> reach the equilibrium again.
> However, even in this case, the temperature change might be too abrupt
> and to not give enough
> time to the replicas volume to contract or expand.
>
> Am I right or I am missing something here?
>
> I would really appreciate if someone can give clarification about this.
>
> All the best,
> MP
>
>
> --
> Dr Massimiliano Porrini
> P. E. Barran Research Group
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> 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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Received on Wed May 11 2011 - 05:30:04 PDT
