Digital simulation molecular dynamics

Phillips, S.C. Essex, J.W. Edge, C.M., Digitally filtered molecular dynamics the frequency specific control of molecular dynamics simulations, J. Chem. Phys. 2000,112, 2586-2597... 

The first task of chemoinformatics is to transform chemical knowledge, such as molecular structures and chemical reactions, into computer-legible digital information. The digital representations of chemical information are the foundation for all chemoin-formatic manipulations in computer. There are many file formats for molecular information to be imported into and exported from computer. Some formats contain more information than others. Usually, intended applications will dictate which format is more suitable. For example, in a quantum chemistry calculation the molecular input file usually includes atomic symbols with three-dimensional (3D) atomic coordinates as the atomic positions, while a molecular dynamics simulation needs, in addition, atom types, bond status, and other relevant information for defining a force field. 

This account highlights some of the recent developments in methods and current applications of classical trajectory simulations of molecular collisions. It has been more than 60 years since the first classical trajectory calculation was attempted on a mechanical calculator and almost 40 years since the first ensembles of trajectories were calculated on a digital computer and, even though the real world is quantum mechanical, classical trajectory simulations continue to play a crucial role in studies of chemical dynamics. The classical approximation, fortunately, is valid for many processes and conditions of interest to chemists, and the Monte Carlo quasiclassical trajectory approach is relatively simple and straightforward to apply. The work reviewed here clearly illustrates that it continues to be used productively, creatively, and widely, to study the details of chemical processes. 

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