Send to

Choose Destination
J Chem Theory Comput. 2009 Jun 9;5(6):1632-9. doi: 10.1021/ct9000685. Epub 2009 May 21.

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

Author information

Information 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.


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‚ÄČ000 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.


Supplemental Content

Loading ...
Support Center