colvar DistanceZ

From: Kevin C Chan (
Date: Tue Nov 25 2014 - 21:03:55 CST

Dear Users,

I am currently using DistanceZ for my colvars definition and everything
goes fine except it does not gives me the value I expect.

I thought DistanceZ was measuring the subtracted vector between the centre
of mass of atoms in the main group and that in the ref group and then
projected it onto the z-axis, in other words only the z component is of the
interest. In my system,
com of main locates at z=40
com of ref locates at z=-55
However the first step (step 0) of colvars.traj gives me -65 for DistanceZ.

As I'm doing the umbrella sampling, it's fine if I change my windows list
according to z=-65 but I'm just curious what DistanceZ was actually

Thanks in advance,
Kevin <javascript:;>

Follow is the input parameters:

colvar {
name ProjectionZ

width 0.25

distanceZ {

 main {
   atomsFile main.pdb
   atomsCol B
   atomsColValue 1.0
 ref {
   atomsFile ref.pdb
   atomsCol B
   atomsColValue 1.0

harmonic {
colvars ProjectionZ
centers 40
forceConstant 4.0

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