AMBER Archive (2008)

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

From: d90223013_at_ntu.edu.tw
Date: Tue Jan 29 2008 - 01:35:08 CST

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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