An Efficient Way to Conserve the Total Energy in Molecular Dynamics Simulations; Boundary Effects on Energy Conservation and Dynamic Properties

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Abstract
Molecular Dynamics simulations of pure water are reported, where the so-called jump correction i.e., inclusion of the Dirac delta force corresponding to the potential discontinuity at cutoff, ensures that the force is the negative gradient of the potential everywhere. Results are compared to those obtained for potentials truncated in the ordinary way and for potentials where the discontinuity is removed by means of a switching function. The jump correction and the switching functions provide excellent conservation of the total energy, and remove the need for temperature scaling at equilibrium. Radial distributions are insensitive to boundary conditions. Translational and rotational diffusion vary considerably with boundary conditions and also with cutoff distance.