[gmx-users] harmonic angle potential
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:
> 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
> 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
> 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.
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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