AMBER Archive (2005)

Subject: Re: AMBER: No exchange among replicas in REMD!

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Mon Dec 19 2005 - 10:35:30 CST

we discussed some of the issues and give references in
Cheng, Cui, Hornak and Simmerling, J. Phys. Chem B 2005, v 109 p 8220

Peng Tao wrote:

> Dr. Carlos Simmerling,
>
> So far I haven't scaled my temperatures series according to my
> simulation system size. I think I have lot of options to do
> temperature spacing for REMD. But I am not sure which one to
> choose. Now I am thinking about linear or exponential relations, which
> sound reasonable.
> The problem is that I don't have any articles talking about this
> subject in hand for reference, and couldn't find one.
> Any suggestions or articles?
>
> Thank you very much.
>
> Best regards,
> Peng Tao
>
>
> On 12/18/05, *Carlos Simmerling* <carlos_at_ilion.bio.sunysb.edu
> <mailto:carlos_at_ilion.bio.sunysb.edu>> wrote:
>
> did you space them according to system size?
>
> Peng Tao wrote:
>
> > I made this temperature spacing according to
> YujiSugitaa,YukoOkamoto's
> > article: Chemical Physics Letters 314, (1999), 141–151
> > Replica-exchange molecular dynamics method for protein folding.
> > Their temperatures for REMD distribute exponentially. That's why my
> > temperatures are far away from each other above 400K.
> >
> > I will set new temperatures more closer to each other, and rerun my
> > simulations.
> >
> > Thanks for help.
> >
> > Best regards,
> > Peng Tao
> >
> >
>
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