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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 02 2004 - 10:53:00 PDT
