AMBER Archive (2004)

Subject: AMBER: question about replica exchange in amber8

From: J. Zhang, Dr (jzhang_at_biophy.nju.edu.cn)
Date: Wed Jun 02 2004 - 04:24:24 CDT

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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