Paper Citing NAMD - Abstract
Meineke, M.A.; Vardeman, C.F.; Lin, T.; Fennell, C.J.; Gezelter, J.D.
OOPSE: An object-oriented parallel simulation engine for molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:252-271, FEB 2005
OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.
