Re: Replica exchange - Temperatures and number of replicas

From: Aron Broom (
Date: Sun Nov 25 2012 - 19:27:42 CST

I've never run these kind of simulations, but is this a system with a
protein of other kind of folded polymer? Because I would think you might
need to apply some kind of restraint to the backbone RMSD in that case,
otherwise unfolding would cause a dramatic change in potential energy which
might preclude swapping? Just a thought.


On Sun, Nov 25, 2012 at 6:06 PM, Siri Søndergaard <>wrote:

> Hi
> I'm trying to run replica exchange simulations with metadynamics and the
> issue is to determine the most suitable temperatures and number of
> replicas. My system contains app. 20.000 atoms and I want around 20% of the
> swaps to be accepted. I tried several combinations of temperatures and
> replicas but only one resulted in an actual swap: T1 = 300, T2 = 350 and
> the number of replicas was 12. This gave a probability of accepted swaps of
> 8%. I think 12 replicas is a quite high number for a small temperature
> difference but if the difference is increased with as little as 50K I get
> no swaps at all. Does anybody have experience setting up these parameters?
> Siri Sondergaard

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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