[MMTK] MMTK - Implementing Shifted Leonard Jones potential

Peter mmtk at maubp.freeserve.co.uk
Wed Jun 9 19:48:31 CEST 2004


Hello Konrad et al.

I have been looking at the Leonard Jones potential force field in MMTK.

As per the documentation,

http://starship.python.net/crew/hinsen/MMTK/Manual/MMTK_20.html

When using a cut off radius (r_cutoff) the potential energy is:

V_LJ(r) = 4*epsilon*((sigma/r)**12-(sigma/r)**6)

if r < r_cutoff, or V_LJ(r)=0 otherwise
where epsilon = LJ_energy, and sigma = LJ_radius

Clearly, if using a cutoff radius then there is a discontinuity in the
potential at the cutoff point (r = r_cutoff).



I would like to use a continuous "Truncated Leonard Jones potential", or
"Shifted Leonard Jones potential" defined as follows:

V_SLJ(r) = V_LJ(r) - V_LJ(r_cutoff)

if r < r_cutoff, or V_SLJ(r)=0 otherwise.

The Leonard Jones potential seems to be defined in 3 python files and
two C files,

MMTK\ForceFields\__init__.py
MMTK\ForceFields\LennardJonesFF.py
MMTK\ForceFields\NonBondedInteractions.py
Src\MMTK_forcefield.c
Src\nonbonded.c    (does actual potential calculation)

The existing LJ forcefield is also tied into the AMBER94 Forcefield.



How would you suggest I go about adding the "Shifted Leonard Jones
potential" to MMTK?

(a) Editing the above files to include it, based on the existing LJ code
(b) Implement it independently of the existing LJ forcefield, basing the
module structure on the Harmonic Oscillator example forcefield.

Thanks

Peter





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