AMBER Archive (2005)

Subject: Re: AMBER: Replica exchange

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Mon Aug 29 2005 - 07:46:52 CDT

Which method for maintaining temperature is recommended for replica
exchange??

Thank you for your answers.

On Sunday 28 August 2005 7:16 am, Carlos Simmerling wrote:
> keep in mind that the number of replicas scales with the
> square root of system size. A peptide with implicit solvent
> may need 10-30 replicas, while explicit solvent in a box large
> enough to unfold may need hundreds of replicas. Read the literature
> to see what people have done. Implicit solvents are faster and much
> cheaper for REMD but they do have limitations. Choosing between
> implicit and explicit solvent (especially for REMD) is
> a difficult decision. Amber9 will have some new REMD features that
> will help with this, but REMD in explicit solvent for all but the
> smallest peptides is not practical unless you have huge computers
> available.
>
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