Re: Relative RMSD constraint

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

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