VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 05 2016 - 08:45:15 CDT

> On Jul 5, 2016, at 9:37 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> On Mon, Jul 4, 2016 at 5:09 PM, 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
>
> peter,
>
> it is not the "force field", but the fore projection on the atoms. for
> the case where the two bonds forming an angle are (near) parallel, the
> standard expression diverges. in fact, for exactly parallel bonds, one
> could pick a random direction to bend the molecule.
>
> to answer bernard's question. if you look into the source code, you'll
> see that NAMD will use an approximation for sin(theta) < 1.0e-6 that
> is suitable for theta equals 0 or pi (n.b. diff = theta - theta0 and
> normal = 1 for CHARMM)
>
Thanks, Axel, for the very useful answer — and apologies to Bernard that I missed the target of the question.
Best,
Peter