From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Jan 19 2016 - 14:40:20 CST
Dr. Eddie,
>From what I understand (hopefully someone on the forum will correct me if I
am wrong), when you do replica exchange simulation, you want your target
replica to stay at the target temperature. All that you are doing is, at
regular intervals, you are seeding this simulation with structures that
have "seen" higher energies, and hence, taken conformations that the target
replica would have taken very long to adopt. This is a way to get this
target replica to converge faster, without really increasing its
temperature.
Hope that made sense.
Regards,
Chitrak.
On Tue, Jan 19, 2016 at 11:35 AM, Dr. Eddie <eackad_at_gmail.com> wrote:
> HI all,
> This isn't a namd-only question but since RE is used by many namd users
> I'm hopeing someone can point me to a good reference. I have a simple
> question:
> Why is replica exchange more efficient than just heating a single system
> up and then cooling it when it gets stuck (one could use the same criteria
> for doing this as RE)?
>
> More precisely, why is it more efficient to have N-replicas at different
> temperatures rather than N-individual runs with different initial
> conditions that are heated/cooled as needed to get over potential barriers?
>
> I would appreciate any references or comments.
> Thanks in advance,
>
> Eddie
>
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