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PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based simulations on system ranging in complexity from simple molecular liquids and crystals to large biomolecular systems. In addition, PINY_MD can perform ab initio molecular dynamics and geometry optimization using plane-wave based generalized gradient (GGA) density functional based representations of the electronic structure combined with the Car-Parrinello propagation scheme.