# [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".

-Grace

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
> > > _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

```