Re: AMBER: No exchange among replicas in REMD!

From: Peng Tao <amberhelp.gmail.com>
Date: Mon, 19 Dec 2005 09:57:30 -0500

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.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), 141151
> > 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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Received on Mon Dec 19 2005 - 15:53:01 PST
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