A Conservation of Energy and Momentum Algorithm Using Switching Potentials Suitable for Molecular Dynamics of Thermodynamical Systems
by
Christopher Gunaseelan Jesudason
Chemistry Department, University of Malaya, 50603 Kuala Lumpur; Laboratory of Physics and Helsinki Institute of Physics, P.O.Box 1100, FIN-02015 HUT, Finland

During a crossover from one 2-body potential to another 2-body via a switching mechanism, such as might be applied for a model of a particle (chemical) reaction at the point of bond formation, energy violations would occur due to finite step size which would determine the trajectory of the particles relative to the potential interactions of the unbonded state by numerical (e.g. Verlet) integration. This problem is overcome by an algorithm which preserves the coordinates of the system for each move, but corrects for energy discrepancies by ensuring both energy and momentum conservation in the dynamics. The algorithm is tested for various reaction models when the algorithm is turned on and off, including the hysteresis loop mechanism in addition to the conventional model used for describing bond formation which does not have any hysteresis potential. The tests involve checking the rate of energy flow out of the MD simulation box; in the equilibrium state, no net rate of flows within experimental error should be observed. Also the temperature and pressure of the box should also be invariant within the range of fluctuation of these quantities.

Date received: December 9, 2006