From: Andrei Tudor (andrei.tudor.1_at_ulaval.ca)
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:
dummyAtom (center of initial coords of the peptide)
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.
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