AMBER Archive (2004)

Subject: Re: AMBER: question about replica exchange in amber8

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jun 02 2004 - 08:58:32 CDT

Dear Dr. Zhang,

how often exchange should be attempted is largely controlled by the size
of your
system as well as the temperature gap between replicas (temperature
coupling
constant too). it should be long enough to allow the temperature to
relax to the
new value. hope this helps.

Guanglei

J. Zhang, Dr wrote:

> Dear Amber users,
>
> When using replica exchange MD in amber8, I am confused at what the appropriate
> value of NSTLIM is, i.e. the parameter that controls the exchange frequency.
>
> Several published values of the exchange frequencies can be found, such as:
> 1) 46-residue three-helix 0.375ps pnas(2003)
> 2) 12-residue beta-hairpin 5 ps jmb(2004)
> 3) 5-residue peptide 0.01ps Sugita (1999)
> 4) amber user guide 100-1000 MD steps
>
> So, it can be seen that the value varies in a broad range. Any one could give
> some suggestions about how to choose it? Any disadvantages of too small and
> too large values?
>
>
> Best Regards,
>
> ---
> J. Zhang, Dr
> Institute of Biophysics
> Nanjing University
>
>
>
>
>
>
>
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