From: Huihui Liu (christina.huihui.liu_at_gmail.com)
Date: Thu Oct 31 2013 - 10:04:23 CDT
Hi,
I have some doubt about the set-up of aMD parameters in NAMD2.9 where there
are three kinds of aMD: aMDd, aMDT, and aMDdual. In the dual boost mode
(aMDdual), two independent boost energies are applied, one on the dihedral
potential and the other on the (Total - Dihedral) potential. Now, I am
using the three modes to find out their different accelerated effects on my
system. I got some notes for parameters setting from the book Computational
Drug Discovery and
Design<http://www.springerprotocols.com/BookToc/doi/10.1007/978-1-61779-465-0?uri=/Abstract/doi/10.1007/978-1-61779-465-0_30>
published
in 2012, i.e.
For aMDd mode, suggested initial parameters are: *E*dihed=<*V*dihed>+4**n*res,
*alpha*dihed=0.8**n*res (*n*res refers to the number of residues in the
protein).
For aMDT mode, suggested initial parameters are: *E*total=<*V*total>+*n*atom/5,
*alpha*dihed=*n*atom/5 (*n*atom is the number of atoms in the system).
But how about the aMDdual mode? What are the suggested initial parameters
for the (Total - Dihedral) potential? Any suggestion is appreciated.
Thanks,
Christina
Tsinghua University, Beijing, China
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