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 a 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.
@article{arxiv.0902.0827,
title = {ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale},
author = {M. J. Harvey and G. Giupponi and G. De Fabritiis},
journal= {arXiv preprint arXiv:0902.0827},
year = {2009}
}