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

TL;DR

ACEMD leverages GPU parallelism to significantly accelerate bio-molecular dynamics simulations, enabling routine microsecond-scale trajectories on cost-effective hardware, thus advancing computational biology research.

Contribution

This paper introduces ACEMD, a GPU-optimized MD simulation program capable of achieving microsecond timescales efficiently and cost-effectively.

Findings

Achieves 40 nanoseconds/day for all-atom protein systems

Runs microsecond-long trajectories on a single workstation with 3 GPUs

Demonstrates practical implications for scientific applications

Abstract

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.