AMBER
The explicit solvent and implicit solvent 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.
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 also on the download page
Benchmark Data
Benchmark data for explicit solvent PME and implicit solvent GB Benchmarks. Details can be found on the AMBER 11 NVIDIA benchmark page courtesy of the San Diego Supercomputing Center.
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Technical Papers And Presentations
- New publications based on AMBER 11 GPU-acceleration work coming soon
- From SC09: Overview of NVIDIA CUDA Support in AMBER- Lessons Learned, Capabilities Gained – Ross Walker, The San Diego Supercomputer Center, from 2009 GPU Technology Conference
- From 2009 GPU Technology Conference: Computational Biophysics and Long Range Electrostatics on GPUs – Scott Le Grand, NVIDIA
- More publications on accelerating molecular dynamics applications using GPUs
- More publications on accelerating quantum chemistry applications using GPUs
Discussion Forums
Interviews / Videos
- SC09 BLOG on NVIDIA nTersect: AMBER Research Code Gets Impressive Gains with NVIDIA CUDA
The Tesla Bio Workbench applications can be deployed on GPU-based desktop personal supercomputers or in data center solutions. Built on the revolutionary massively parallel CUDA architecture, these solutions are designed to accelerate the pace of computational science.
RECOMMENDED HARDWARE CONFIGURATION
| Desktop Workstation Configuration | Data Center Configuration |
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WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk
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DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations
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