**From:** Giacomo Fiorin (*giacomo.fiorin_at_gmail.com*)

**Date:** Sat Apr 16 2011 - 10:33:23 CDT

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Hello Hyon, if the coordinates are the ones you wrote during the simulation,

the CM computed for your group "main" is (-1, 0, 0).

Obviously, if you're using wrapAll, that will change the coordinate of one

atom or the other (depending on where the origin of the box is). I suggest

that you disable wrapAll and use just wrapWater (unless you're considering

atoms within water molecules).

Giacomo

---- ----

Giacomo Fiorin - Postdoctoral Researcher

ICMS - Institute for Computational Molecular Science - Temple University

1900 N 12 th Street, Philadelphia, PA 19122

giacomo.fiorin_at_temple.edu

---- ----

On Sat, Apr 16, 2011 at 10:57 AM, Hyonseok Hwang <danggi_at_gmail.com> wrote:

*> Dear all,
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*>
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*> I know that in the NAMD userguide there is some comments about the the
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*> center of mass calculations between two groups spanning different
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*> molecules in the colvar , but I don't quite understand about that. So
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*> I would like to give an example as my question.
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*>
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*> I have two atoms and I want to calculate the distance between the
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*> center of mass of the two atoms (which are bonded to different
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*> molecules and have the same mass) and a reference dummy atom. Then I
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*> may use the colvar module shown below:
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*>
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*> colvar {
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*> name test
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*>
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*> distance {
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*> main {
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*> two atoms
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*> }
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*> ref {
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*> dummyAtom (0.0, 0.0, 0.0)
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*> }
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*>
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*> }
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*> }
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*>
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*> Assume that the coordinates of the two atoms are (12.0, 0.0, 0,0) and
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*> (-14.0, 0.0, 0.0), respectively, and the the box size in x direction
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*> in 15 A.
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*> Then, to get the distance, the colvar module will calculate the center
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*> of mass of the two atoms in main. There comes my question. What is the
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*> center of mass of the two atoms in this case? Is the CM (14.0, 0.0,
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*> 0.0) or (-1.0, 0.0, 0.0)? I use periodic boundary conditions and the
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*> keyword "wrapall"
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*>
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*> Thank you in advance.
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*>
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*> Hyon
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*>
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*>
*

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