From: Julius Su (jsu_at_caltech.edu)
Date: Mon May 10 2004 - 13:09:14 CDT
Hello,
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
defined?
1. off-diagonal nonbond interactions (e.g. LJ)
2. bond list, for each atom access to the coords of atoms bonded to
it.
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.
Thanks,
Julius
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:38 CST