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From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Mon, 17 Sep 2007 10:04:46 -0400

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.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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Received on Wed Sep 19 2007 - 06:07:20 PDT

Date: Mon, 17 Sep 2007 10:04:46 -0400

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.gmail.com> wrote:

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Received on Wed Sep 19 2007 - 06:07:20 PDT

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