[gmx-users] harmonic angle potential

[Grace Brannigan]

Hi,

I'm trying to use Gromacs for simulations of short Lennard-Jones type
chains. I already have home-made MC code. When I compare Gromacs'
assesment of the potential energy with that of my own code, for one
configuration of two 5mers, the values of the bond angle potential
disagree.

I was looking through the Gromacs source code to make sure I had
consistent potentials, and I noticed that in the function "angles", the
sum goes over the number of bonds. I guess this makes sense for the
forces, but it seems weird for the potential; it seems like it should go
over the number of angles (i.e., num_bonds - 1). Is it possible that one
angle is being counted twice? Maybe I'm misunderstanding how this function
works...

Has anybody else had this problem? I'm hoping there's a simple thing I'm
doing wrong but I haven't found it in my own code.

-Grace