VMD-L Mailing List
From: Mr Bernard Ramos (bgrquantum_at_REMOVE_yahoo.com)
Date: Fri Jul 15 2016 - 19:39:14 CDT
Thanks Peter and Axel.
On Tuesday, July 5, 2016 5:09 AM, Peter Freddolino <petefred_at_umich.edu> wrote:
Why do you think the "force field" is proportional to 1/sin(a)? The magnitude of the force is proportional to (a-a0), as should be clear from the form of the potential.
> On Jul 3, 2016, at 11:56 PM, Mr Bernard Ramos <bgrquantum_at_REMOVE_yahoo.com> wrote:
> Hi all!
> 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?
> Thank you.