Re: Fixing COM of one atom in selection and letting the other move

From: Vermaas, Joshua (
Date: Tue Feb 14 2017 - 18:12:38 CST

The distance Z colvar is relative. So the position of main along the z axis relative to ref. If your dummy is where you want it to be, you indeed give 0.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory<>

On Feb 14, 2017, at 11:15 AM, Life Sciences Inc <<>> wrote:

Hi all

I am trying to fix the center of mass of one of my selection in lipid bilayer say phosphate atoms, and my protein which is inserted inside the lipid bilayer in z direction, I want the com of protein selection and lipid bilayer selection to be exactly the same after equilibration of my system, for this purpose I have used colvars , can anyone tell me am I going in the right direction my input for colvar is as follows and also let me know if I am giving 0.0 with centers parameter my protein selection will be at 0 with respect to lipid selection or do I have to give the 7.218 for centers value?

colvarsTrajFrequency 100

colvar {
  name d

  width 1.0 # typical displacement is set to 1 Angstrom

  distanceZ {
    ref {
      dummyAtom (0.076, 0.416, 7.218) # fixed position for ref atoms from bilayer
    main {

      # group definition: selection of the protein, which I need to move towards the com of the ref selection
      psfSegID P1
      atomNameResidueRange CA 1-12


harmonic { # Define a moving harmonic restraint
  colvars d # acting on 1 colvars

  centers 0.0 #
  forceConstant 10.0 # unit is kcal/mol/[width]^2


Thanks in advance

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