ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale [article]

M. J. Harvey, G. Giupponi, G. De Fabritiis
2009 arXiv   pre-print
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 bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run
more » ... microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.
arXiv:0902.0827v1 fatcat:ldqlm4o4fnh3tcf54jzjbdynue