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Recommended Hardware• See the following page for continuous updates:http://ambermd.org/gpus/recommended_hardware.htm#hardwareSAN DIEGO SUPERCOMPUTER CENTER36
DIY 4 GPU SystemAntec P280 Black ATX Mid Tower Casehttp://tinyurl.com/a2wtkfr$126.46GIGABYTE GA-990FXA-UD7AM3+ AMD Motherboardhttp://tinyurl.com/b8yvykv$216.00SILVERSTONE ST1500 1500WATX12V/EPS12V Power Supplyhttp://tinyurl.com/alj9w93$299.99AMD FX-8350 Eight Core CPUhttp://tinyurl.com/b9teunj$189.15Corsair Vengeance 16GB(2x8GB) DDR3 1600 MHzDesktop Memoryhttp://tinyurl.com/amh4jyu$96.87Seagate Barracuda 7200 3 TB7200RPM Internal Bare DriveST3000DM001http://tinyurl.com/a4ccfvj$139.994of EVGA GeForce GTX 6804096 MB GDDR5http://tinyurl.com/d82lq8d$534.59 eachOr K20X or GTX TitanTotal Price : $3206.82Note cards in this system run at x8 so you can only run single GPU AMBER runs (but you can run 4 simultaneously at fullspeed) – If you want to be able to run MPI 2xGPU runs then only place 2 cards in the x16 slots.SAN DIEGO SUPERCOMPUTER CENTER37
Page 1 and 2: AMBER and Kepler GPUsJulia Levites,
Page 3 and 4: What is Molecular Dynamics?• In t
Page 5 and 6: Force FieldsSAN DIEGO SUPERCOMPUTER
Page 7 and 8: The AMBER Development TeamA Multi-I
Page 11 and 12: Why do we need Supercomputers?Lots
Page 13 and 14: Moving Molecular DynamicsForward?(a
Page 15 and 16: The Problem(s)• Molecular Dynamic
Page 17 and 18: Requirements• Any implementation
Page 19 and 20: Project Info• AMBER Website: http
Page 21 and 22: Version History• AMBER 10 - Relea
Page 23 and 24: Precision ModelsSPSP - Use single p
Page 25 and 26: Running on GPUs• Details provided
Page 27 and 28: 800.00700.00600.00500.00400.00300.0
Page 29 and 30: Explicit Solvent Benchmark(Cellulos
Page 32: Interactive MD?• Single nodes are
Page 35: Graphics cardQuadro9%Other1%Don't k
Page 39 and 40: Clusters# of CPU sockets 2Cores per
Page 41 and 42: AMBER User Survey - 2011GPU Momentu
Page 43 and 44: GPU Accelerated Apps MomentumKey co

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