implementing angle dependent non-bonded interaction?

From: Julius Su (
Date: Mon May 10 2004 - 13:09:14 CDT


I'd like to add an angle dependent non-bonded interaction to NAMD of the
form --

  E = (1 + (cos theta)^2) exp(-a r)

where theta is the angle between two vectors:
  (1) vector joining atom1 and atom2
  (2) normal vector defined by the plane containing atom2 and its two
bonded neighbors
      (e.g. water).

Could someone point me to where the following files/functions are

  1. off-diagonal nonbond interactions (e.g. LJ)
  2. bond list, for each atom access to the coords of atoms bonded to
  3. parsing of parameter file; user defined parameters (e.g. force
field file)

This potential would allow us to implement a proton dynamics force field
our group is developing.



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