AMBER Archive (2007)

Subject: Re: AMBER: replica exchange simulation

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 17 2007 - 09:04:46 CDT

when you derive the exchange probability equation, you need to insert the
limiting distribution of the replica into the equation. In std temperature
replica exhgance, you insert the Boltzmann probability, thus you need to
be running under conditions that generate that. If not, you will need to
rederive
the equations. We show an example of changing the probability eqn for one
replica and leaving the others in

Roitberg, A., Okur, A. and Simmerling, C., "*Coupling of Replica Exchange
Simulations to a non-Boltzmann structure reservoir*", J. Phys. Chem. B,
111:2415-2418 (2007)

On 9/15/07, Ji-Lai Li <jlutcc_at_gmail.com> wrote:
>
> Dear Amber Users:
> I have one question on the replica exchange simulation. Can you give
> me the answer? Many thanks in advance.
>
> Suppose there are N replicas (1,…,M,….N) in replica exchange simulations.
> The replica M corresponds to the temperature of interest, i.e. we want to
> compute the thermal averages for the replica M simulated at the temperature
> TM. Usually, each replica is simulated using canonical ensemble. Is it
> possible to replace canonical simulation in one of the replicas, say n
> (1<=n<=N, but n≠M), with microcanonical simulation without violating the
> canonical distributions in other replicas, including the replica M?
>

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