question about Distance XY

From: Song, Hyundeok (songhk) (
Date: Mon Sep 12 2011 - 23:27:05 CDT

Dear NAMD users
First I red many postings about Distance XY from mailing list, but I didn't understand some parts.

I want to restrain an ion on XY plane such as the circle of radius 10A
ex: reference - atom groups from 1 to 32.
      main - one ion, number 50
      xydistane between a reference group and an ion.

I included my colvar script. Please read my colvar script. If my script has a problem, please let me know.
I have two questions.
1. Does the harmonic force will not apply as long as an ion is inside the boundary(10A from cm of references)?

2. Which value do I choose for 'centers', initial center of restraint ?
Can I set 'centers' as '0' (A) ?

Initially an ion is inside the circle, and if the harmonic force is applied only if an ion try to escape the circle of radius 10A, setting up 'centers' less than 10A is fine.
I didn't specify the lowerboundary because it's zero.



************************colvar script ****************************************
colvar {
   name ProjectionXY
   upperboundary 10.0
   upperwallconstant 10.0

   distanceXY {
      ref {
         atomNumbersRange {1 - 32 }
      main {
         atomnumbers { 50 }

harmonic {
colvars ProjectionXY
centers 0.0
forceConstant 10

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