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Our previously developed polarizable electrostatic model is applied to isolated N-methylacetamide (NMA) and to three hydrogen-bonded configurations of the NMA dimer. Two versions of the model are studied. In the first one (POL1), polarizability along the valence bonds is described by induced bond charge increments, and polarizability perpendicular to the… (More)

The stability of a general molecular dynamics (MD) integration scheme is examined for simulations in generalized (internal plus external) coordinates (GCs). An analytic expression is derived for the local error in energy during each integration time step. This shows that the explicit dependence of the mass-matrix on GCs, which makes the system's Lagrange… (More)

With currently used definitions of out-of-plane angle and bond angle internal coordinates, Cartesian derivatives have singularities, at "r2 in the former case and in the latter. If either of these occur during molecular mechanics or dynamics simulations, the forces are not well defined. To avoid such difficulties, we provide new out-of-plane and bond… (More)

A new electrostatic model for the calculation of infrared intensities in molecular mechanics and molecular dynamics is presented. The model is based on atomic charges, atomic charge fluxes, and internal coordinate dipoles and their fluxes. The internal coordinate dipoles are used instead of atomic dipoles, thus simplifying the derivation of parameters. The… (More)

The rapid development of computers in recent years has brought increasingly complex compounds into the range of high level ab-initio calculations. Such calculations produce valuable results which In many cases would be difficult or even impossible to obtain, with comparable accuracy, in any other way (Fogarasi & F'ulay, Annu. Rev. Thus, it is highly… (More)

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