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 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/
> --
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 06:00:03 PDT
