Replica exchange, colvars & harmonic restraints

From: Andrei Tudor (
Date: Mon Jul 29 2013 - 13:36:22 CDT


I want to run a replica exchange simulation with my protein system. I am pretty sure I got the configuration of the replica exchange part working, but I want to use colvars and harmonic restraints to keep the protein in the center of the box (using it's center of mass).

I have never used colvars and I find them quite confusing. I know I have to create a group for the atoms forming my protein and use somehow the center of mass of that selection.

I want to use harmonic restraints to let the center of mass oscillate a bit, but not by much. Let's say 5 A. How does one make the config file of the colvars?

I am thinking of doing it something like this:

colvar {
        name COM
                 group1 {
                 group2 {
                       dummyAtom (center of initial coords of the peptide)

harmonic {
           colvars COM
           centers 0 ?????
           forceConstant 10.0 ???????

Does this look any good? Where I put the question marks, it means that I don't know why to put the values I put. I don't really understand the harmonic options.
Also if I calculate the coords of the center of the peptide in vmd, is that what I should put as the dummyAtom coordinates?

Any help will greatly appreciated.

Thank you,

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