AMBER Archive (2006)

Subject: Re: AMBER: Replica exchange

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Jul 17 2006 - 09:18:57 CDT

Hi Austin,

I think it's better to have the replicas separately equilibrated to
their target temperatures before you commit them to the exchange. Is
there any particular reason that you want to cold start all of them
other than convenience?

Guanglei

Austin B. Yongye wrote:
> Dear amber users,
> I am running some replica exchange simulations and split between two options:
>
> Is it better to
> 1. Equilibrate a single structure in a solvent to a particular temperature
> eg 300K and then generate the replicas from this point with different
> target temperatures, irest=1, ntx=5, etc?
>
> 2. Start with all the replicas at 0K and give each replica a different
> target temperature, irest=0, ntx=1, etc?
>
> Thanks,
> austin-
>
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