From SklogWiki
Jump to navigation Jump to search

PINY_MD is a multipurpose, object-oriented molecular simulation package. PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based (classical) simulations on system ranging in complexity from simple molecular liquids (.e.g, water, ammonia, liquid alkanes) and crystals (e.g., ice) to large biomolecular systems such as the HIV-1 protease in solution. Long range electrostatic forces are treated using smooth particle-mesh Ewald summation techniques. Biomolecular systems can be constructed using the code's built-in molecular building tools. 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.

Simulations can be performed in a number of statistical ensembles, including the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) with isotropic or fully flexible cell variations. Ensembles are generated using well established methodology developed by the principle authors. All molecular dynamics simulation types can be performed using multiple time scale integration techniques also developed by the principle authors. Nuclear quantum effects can be studied as well using the principle authors' path integral molecular dynamics methodology. Path integrals can be performed for both force-field based and ab initio calculations. Geometries such as surfaces, clusters and wires can also be studied.


  1. Mark E. Tuckerman, D. A. Yarne, Shane O. Samuelson, Adam L. Hughes, and Glenn J. Martyna "Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers", Computer Physics Communications 128 pp. 333-376 (2000)