[gmx-users] harmonic angle potential

Grace Brannigan gbrannig at physics.ucsb.edu
Mon Sep 20 07:47:34 CEST 2004

I'm assuming Gromacs uses the potential V = k (theta - theta0)^2 /2, where
k is the value I put into the topology. I have defined four bonds and
three angles per molecule (that's why I was worried about the "angles"
function summing over bonds rather than angles). As far as I can tell,
Gromacs overcounts and is off by about 25%. My program and g_angle agree
on the average angle, etc, and if I just plug the avg. value of theta in
to the above formula (and multiply by 3 angles), I get back what my
program spits out.

So it seems like there must be some difference in how Gromacs and I are
evaluating the potential, yet the evaluation seems pretty straightforward.
Oh, I also checked to make sure I'm using function type "#1".


On Sun, 2004-09-19 at 22:56, Grace Brannigan wrote:
> 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.
Are you sure your topology is correct? For a 5 mer you should define 4
bonds and three angles.

Then there is the half in the definition of the potential.
> > -Grace
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