question on the center of mass calculation in colvar

From: Hyonseok Hwang (
Date: Sat Apr 16 2011 - 09:57:16 CDT

Dear all,

I know that in the NAMD userguide there is some comments about the the
center of mass calculations between two groups spanning different
molecules in the colvar , but I don't quite understand about that. So
I would like to give an example as my question.

I have two atoms and I want to calculate the distance between the
center of mass of the two atoms (which are bonded to different
molecules and have the same mass) and a reference dummy atom. Then I
may use the colvar module shown below:

colvar {
     name test

    distance {
        main {
            two atoms
        ref {
            dummyAtom (0.0, 0.0, 0.0)


Assume that the coordinates of the two atoms are (12.0, 0.0, 0,0) and
(-14.0, 0.0, 0.0), respectively, and the the box size in x direction
in 15 A.
Then, to get the distance, the colvar module will calculate the center
of mass of the two atoms in main. There comes my question. What is the
center of mass of the two atoms in this case? Is the CM (14.0, 0.0,
0.0) or (-1.0, 0.0, 0.0)? I use periodic boundary conditions and the
keyword "wrapall"

Thank you in advance.


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