AMBER Archive (2004)

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

From: xiaolin cheng (cheng_at_ilion.bio.sunysb.edu)
Date: Wed Jun 02 2004 - 09:23:30 CDT


Hi, Zhang,

I have been using kinetic energy fluctuation metric and force metric
criterion introduced by Mountain, Straub and Thirumalai to evaluate the
relaxation time between exchange trials.

Using Amber8, with the temperature coupling constant of 1.0, the minimum
relaxation time of 0.5 ps seems to be required to reach equilibrium after
each exchange for a test system of about 400 atoms.

If interested, you can take a look at the following paper and references
therein about the method,

Straub, J. E.; Thirumalai, D. Proteins 1993, 15, 360.

Xiaolin

----- Original Message -----
From: "J. Zhang, Dr" <jzhang_at_biophy.nju.edu.cn>
To: <amber_at_scripps.edu>
Sent: Wednesday, June 02, 2004 5:24 AM
Subject: AMBER: question about replica exchange in amber8

> 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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