swMATH ID: 21783
Software Authors: Harvey M., Giupponi G., De Fabritiis G.
Description: ACEMD: Accelerated molecular dynamics simulations in the microseconds timescale. 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.
Homepage: http://pubs.acs.org/doi/abs/10.1021/ct9000685
Related Software: CUDA; NAMD; AMBER; CHARMM; Gromacs; MUPHY; Scotch; METIS; Hemelb; OpenMM; PuReMD; LAMMPS; IMD; DESMOND; CPMD; GPUTeraSort; BEAST; PBPI; Seq-Gen; RAxML
Cited in: 3 Publications

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