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During a crossover via a switching mechanism from one 2-body potential toanother as might be applied in modeling (chemical) reactions in the vicinity ofbond formation, energy violations would occur due to finite step size whichdetermines the trajectory of the particles relative to the potentialinteractions of the unbonded state by numerical (e.g. Verlet) integration. Thisproblem is overcome by an algorithm which preserves the coordinates of thesystem for each move, but corrects for energy discrepancies by ensuring bothenergy and momentum conservation in the dynamics. The algorithm is tested for ahysteresis loop reaction model with an without the implementation of thealgorithm. The tests involve checking the rate of energy flow out of the MDsimulation box; in the equilibrium state, no net rate of flows withinexperimental error should be observed. The temperature and pressure of the boxshould also be invariant within the range of fluctuation of these quantities.It is demonstrated that the algorithm satisfies these criteria.

Effective conservation of energy and momentum algorithm using switching  potentials suitable for molecular dynamics simulation of thermodynamical  systems