AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers

Abstract

A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE… (More)
DOI: 10.1002/jcc.540140307

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