[gmx-users] harmonic angle potential

Marcos Villarreal arloa at dqb.fcq.unc.edu.ar
Mon Sep 20 13:38:23 CEST 2004

On Sunday 19 September 2004 17:56, 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.
> -Grace

In calculating the potential, gromacs takes the difference betwen the actual 
angle and the reference angle value in radians,  not in degrees. Maybe there 
is the difference.


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