**From:** Hyonseok Hwang (*danggi_at_gmail.com*)

**Date:** Sat Apr 16 2011 - 09:57:16 CDT

**Next message:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Previous message:**mon_sharma_at_research.iiit.ac.in: "Re: NAMDenergy calculations for nucleic acid systems"**Next in thread:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Reply:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Reply:**Jérôme Hénin: "Re: question on the center of mass calculation in colvar"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

Hyon

**Next message:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Previous message:**mon_sharma_at_research.iiit.ac.in: "Re: NAMDenergy calculations for nucleic acid systems"**Next in thread:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Reply:**Giacomo Fiorin: "Re: question on the center of mass calculation in colvar"**Reply:**Jérôme Hénin: "Re: question on the center of mass calculation in colvar"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Mon Dec 31 2012 - 23:20:09 CST
*