colvars angle centerReference

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Fri Dec 05 2014 - 15:00:44 CST

Hi,

I'm having some trouble using an "angle" colvar with "centerReference
on". I think this used to work.

As a test, I define a "distance" colvar by:

colvar {
   name distFixed

   distance {
      group1 {
         atomNumbers 1
         centerReference on
         refPositions (3,0,0)
      }
      group2 {
         atomNumbers 68
         centerReference on
         refPositions (0,0,0)
      }
   }
}
I expect that this distance is always 3.0, and indeed it is.

However, for "angle" colvar, it doesn't seem to work like this. I
would expect the following to always give 90, but it does not.
colvar {
   name phi6

   angle {
      group1 {
         atomNumbers 1
         centerReference on
         refPositions (1,0,0)
      }
      group2 {
         atomNumbers 34
         centerReference on
         refPositions (0,0,0)
      }
      group3 {
         atomNumbers 68
         centerReference on
         refPositions (0,0,1)
      }
   }
}

Is this a bug, or is there something that I'm missing?

Thanks,
Jeff

–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

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