From: Alexander Predeus (predeus_at_gmail.com)
Date: Wed Aug 17 2011 - 02:31:56 CDT
Jiyong,
First of all, I don't believe you have the formula right, this seems
like a sum of multiple relative RMSD constraints with different
offsets.
As for relative RMSD constraint, you can do it using colvar module.
Define 2 different colvars using rmsd component:
http://www.ks.uiuc.edu/Research/namd/2.8/ug/node55.html#SECTION0001322150000000000000
and then add a harmonic restraint to (var1-var2-offset)
-- Alex Predeus
Michigan State University
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:43 CST