You should look at work by Angel Garcia on this topic. He has done this. It
is not supported in Amber, and unless one wishes to study pressure
dependence it likely is not needed. If one only uses remd to optimize the
low T ensemble then NVT REMD is usually sufficient.
On May 11, 2011 7:33 AM, "Massimiliano Porrini" <M.Porrini.ed.ac.uk> wrote:
Dear Dan,
Thanks a lot for your reply.
But still I do not get the answer to my question and
probably I should read your articles to get it (I must say I have already
carefully read the Sugita and Okamoto work).
I explain what I meant with an example.
As you wrote we relax every replica within NPT ensemble (let's assume
P = 1 atm).
Let's consider the first two replica for simplicity at the beginning
of the run, with their own
temperature (T) and volume (V) values (obtained from the aforesaid
relaxation):
- Rep1: T1 and V1
- Rep2: T2 and V2
and let's assume T2 > T1, thus we have V2 > V1.
If the temperatures are swapped between these two replicas and we are
running
in a NVT ensemble, the systems will end up having a new temperature
"not compatible"
with the actual volume, which should change accordingly.
Specifically, after the exchange, V2 should contract whereas V1 should
expand, but as we have
frozen the initial volumes (by using NVT), these processes are not allowed.
I hope I wrote more clearly what I meant and I apologise if the
answers are in your papers.
All the best,
Max
2011/5/11 Daniel Sindhikara <sindhikara.gmail.com>:
> Since AMBER uses a velocity rescaling factor upon exchange, the replicas
are
> in equilibrium at t...
--
Dr Massimiliano Porrini
P. E. Barran Research Group
Institute for Condensed Matter and Complex Syste...
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Received on Wed May 11 2011 - 06:00:05 PDT
