VMD-L Mailing List
From: Mr Bernard Ramos (bgrquantum_at_REMOVE_yahoo.com)
Date: Sun Jul 03 2016 - 22:56:38 CDT
The potential for the angle-vibration potential in CHARMM is V = k(a - a0)^2. Its corresponding force field is proportional to 1/sin(a) which blows up when a approaches \pi or when the molecule is in linear arrangement. I am wondering how NAMD calculates the angle-bending potential of a linear molecule such as carbon dioxide when it the force vector is singular at a equal to \pi?