AMBER Archive (2008)

Subject: Re: AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jan 29 2008 - 06:21:37 CST

this is really too involved for the email list. in general replicas
should probably not be spaced equally. are you doing MD simulations
first to determine your energy vs temperature slope?
the range of temperature is an open research problem. the
spacing should probably be exponential, although several
people have proposed different schemes. We often introduce extra
replicas near the Tm. Also read papers by Garcia, Hansmann and
see the description and references in one of our early replica papers that
addressed spacing:
Cheng, X., Cui, G., Hornak, V. and Simmerling, C., *"Modified Replica
Exchange Simulation Methods for Local Structure Refinement"*. J. Phys. Chem.
B, 109, 8220-8230 2005

On Jan 29, 2008 2:35 AM, <d90223013_at_ntu.edu.tw> wrote:

> Hi,
> Even though I know that my question probably will not have an absolute
> answer after searching, reading so many literatures, and performing
> the REMD simulations. For example, I have read many of Prof. Yuko
> Okamoto's paper about the principle and applications of REMD. Also,
> I've done a REMD simulation of a small peptide in explicit water.(32
> replicas, temperatures were set up equally separated at the range of
> 300-480K) I'd still like to ask is there any suggestion about how to
> change the temperature spacing and range after I found that the
> acceptance ratios of most of the pairs of temperature are below 10%?
> Any suggestions will be appreciated.
>
> Dr. Yi-Ming Cheng
>
> ========================
> Department of Chemistry,
> National Taiwan University
> personal site: http://mx.nthu.edu.tw/~ymcheng/>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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