Accelerating molecular dynamic simulation on graphics processing units

2009/02/03 by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan +6 · 6 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · Computer Science · Chemistry · Mathematics · #Protein Structure and Dynamics #Enzyme Structure and Function #Algorithms and Data Compression #Graphics #Computer science #Graphics processing unit #Computational science #General-purpose computing on graphics processing units #Molecular dynamics #Field (mathematics) #Molecular graphics #Atom (system on chip) #CUDA #Central processing unit #Computer graphics #Parallel computing #Computer graphics (images) #Chemistry #Computational chemistry #Computer hardware #Mathematics

paper · doi:10.1002/jcc.21209

openalex publication_date 2009/02/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

Abstract

We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core.

Citations

• TestU01
• A Note on the Generation of Random Normal Deviates
• Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece

Cited by

• Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU
• Taming the complexity of protein folding
• Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
• Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment
• OpenMM: A Hardware-Independent Framework for Molecular Simulations
• Folding@home [wikipedia]

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• Harvesting graphics power for MD simulations