Both explicit solvent Particle Mesh Ewald (PME) Molecular Dynamics and implicit solvent Generalized Born (GB) simulations in AMBER have been accelerated using CUDA-enabled GPUs. Paired with a Tesla GPU computing solution built on the CUDA architecture, it enables more than 10x speedup compared to a single quad-core CPU.

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Download and Installation

• Download AMBER 11 (supports CUDA GPUs)
• Implicit solvent Generalized Born simulations
• Explicit solvent PME simulations in NVE, NVT, and NPT canonical ensembles
• Installation instructions are here.

Benchmark Data

The following charts show the acceleration and the scalability when running the explicit solvent PME and implicit solvent GB Benchmarks on a six-core CPU versus Tesla C2070 and Tesla M2090. Details can be found on the AMBER 11 NVIDIA benchmark page courtesy of the San Diego Supercomputing Center.

Technical Papers, News And Presentations

• New publications based on AMBER 11 GPU-acceleration work coming soon
• New Flagship Tesla M2090 CPU Sets Record for AMBER Molecular Dynamics Simulation
• "Redesigning Molecular Dynamics for GPUs and GPU Clusters" by – Scott Le Grand, NVIDIA, GTC 2010
• "Bringing GPUs to Mainstream Molecular Dynamics Packages" by – Ross Walker, The San Diego Supercomputer Center , GTC 2010
• Overview of NVIDIA CUDA Support in AMBER- Lessons Learned, Capabilities Gained – Ross Walker, The San Diego Supercomputer Center, from 2009 GPU Technology Conference, SC09.
• Computational Biophysics and Long Range Electrostatics on GPUs – Scott Le Grand, NVIDIA, GTC 2009.

CUDA-Acceleration in Related Verticals

• Accelerating Molecular Dynamics applications using GPUs
• Accelerating Quantum Chemistry applications using GPUs

Discussion Forums

• GPU computing communities on GPUcomputing.net

Interviews / Videos

• GPU Technology Conference 2010, video from keynote speech by NVIDIA CEO, Jen-Hsun Huang
• SC09 BLOG on NVIDIA nTersect: AMBER Research Code Gets Impressive Gains with NVIDIA CUDA

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