Paper Citing NAMD - Abstract
Straatsma, T.P.; McCammon, J.A.
Load balancing of molecular dynamics simulation with NWChem
IBM SYSTEMS JOURNAL, 40:328-341, 2001
NWChem is a computational chemistry software suite developed for massively parallel computers in the W. R. Wiley Environmental Molecular Sciences Laboratory at the U.S. Department of Energy's Pacific Northwest National Laboratory. This software integrates a range of modules for computational chemistry applications, including classical molecular dynamics simulations and quantum mechanical calculations. This contribution provides details of the classical molecular dynamics module and focuses on issues related to load balancing on massively parallel computers, in particular the ISM SPN and the Gray T3E (TM) as examples of distributed and shared memory massively parallel architectures. The implementation of the molecular dynamics module of NWChem is based on a domain decomposition of the chemical system, faking advantage of the distribution of data to reduce the memory requirements and the locality of intermolecular interactions to reduce the communication requirements. This approach results in a more complex implementation because of the requirement of periodic atomic reassignments and the need for sophisticated load-balancing techniques.
