Re: [AMBER] Temperature-Based Replica Exchange: Number of Replicas

From: Cruzeiro,Vinicius Wilian D <>
Date: Wed, 21 Mar 2018 23:37:47 +0000

Hello Jason,

The number of replicas required to cover a given temperature range increases with the total number of atoms. Therefore, for a system as large as yours (and mainly in explicit solvent) T-REMD becomes impractical because the number of replicas required for a reasonable exchange rate would have to be very large.

In order to check if a given distribution of temperatures is good, you can run a short simulation and check your rem.log file.

I have seen publications in which people use Hamiltonian-REMD instead of T-REMD for large system in order to have a good and efficient temperature sampling. I know they scale the Hamiltonian of each replica to a different effective temperature in order to mimic what happens in T-REMD and good exchange rates are obtained and with a reasonable number of replicas. I have never done calculations like this before though, therefore I don’t know the technical details.


Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633<tel:+1(352)846-1633>

On Mar 21, 2018, at 6:16 PM, Jason Ku Wang <<>> wrote:

Hi AMBER community!

I'm interested in running temperature-based replica exchange for a soluble
protein of ~140,000 atoms in a periodic box with explicit solvent.

I'm having trouble determining the number of replicas and the corresponding
temperature distribution. Are there any resources/protocols that you have
found helpful for determining the temperature distribution?

Furthermore, how does one know that a given temperature distribution is a
good one?

Thanks in advance!
Jason Wang
Stanford University, Class of 2018<>

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Received on Wed Mar 21 2018 - 17:00:02 PDT
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