Paper Citing NAMD - Abstract
Harvey, M. J.; Giupponi, G.; De Fabritiis, G.
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1632-1639, JUN 2009
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein systems with over 23 000 atoms. We provide a validation and performance evaluation of the code and run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. We believe that microsecond time scale molecular dynamics on cost-effective hardware will have important methodological and scientific implications.
