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
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Received on Wed May 11 2011 - 04:30:02 PDT
