ACEMD

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.


References in zbMATH (referenced in 7 articles )

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  1. Trȩdak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.: Efficient implementation of the many-body reactive bond order (REBO) potential on GPU (2016)
  2. Pal, Anirban; Agarwala, Abhishek; Raha, Soumyendu; Bhattacharya, Baidurya: Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions (2014) ioport
  3. Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel; Stamatakis, Alexandros; Shi, Guochun; Kindratenko, Volodymyr: Fine-grain parallelism using multi-core, cell/BE, and GPU systems (2012) ioport
  4. Bisson, Mauro; Bernaschi, Massimo; Melchionna, Simone: Parallel molecular dynamics with irregular domain decomposition (2011)
  5. Colberg, Peter H.; Höfling, Felix: Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision (2011) ioport
  6. Harvey, M. J.; De Fabritiis, G.: Swan: A tool for porting CUDA programs to OpenCL (2011) ioport
  7. Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel: Fast analysis of molecular dynamics trajectories with graphics processing units -- radial distribution function histogramming (2011)