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.
Bernard

    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.
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