VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Jul 04 2016 - 16:09:39 CDT

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.
Best,
Peter

> 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.
>
> Bernard