ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
M J Harvey1, G Giupponi1, G De Fabritiis1
1Information and Communications Technologies, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom, Department de Fisica Fundamental, Universitat de Barcelona, Carrer Marti i Franques 1, 08028 Barcelona, Spain, and Computational Biochemistry and Biophysics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain.
Abstract:
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.
