AW: Replica exchange, colvars & harmonic restraints

From: Norman Geist (
Date: Tue Jul 30 2013 - 00:38:02 CDT



may I ask why you want to do this? What's the reason for your need to keep
the protein in the center of the box?


Norman Geist.


Von: [] Im Auftrag
von Giacomo Fiorin
Gesendet: Montag, 29. Juli 2013 23:23
An: Andrei Tudor
Betreff: Re: namd-l: Replica exchange, colvars & harmonic restraints


Hello Andrei, your configuration looks correct to keep the distance between
the protein's COM and the origin (or the center of your choice).


Regarding the two values, obviously you want the center of the harmonic
potential to be zero, to keep the distance low.


Regarding the force constant, it depends on how big is your protein or
peptide: start with 10, and if peptide still drifts too much for your taste,
increase it until the drift stops.




On Mon, Jul 29, 2013 at 2:36 PM, Andrei Tudor <>


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

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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