Aplicações de dinâmica molecular rodam tranquilamente na arquitetura massivamente paralela das GPUs NVIDIA. Nos gráficos abaixo ressaltamos o trabalho executado em VMD e também pacotes de software de dinâmica molecular como NAMD e HOOMD.
 |
 |
| Colocação de íons em VMD Stone, Phillips, Hardy, Schulten |
HOOMD em 1 GPU NVIDIA supera 16 núcleos de CPU rodando LAMMPs Anderson, Lorenz, Travesset |
 |
|
Download Molecular Dynamics Software for CUDA
- Learn about GPU Acceleration in VMD
- NAMD 2.7 Beta 2 including CUDA Acceleration
- HOOMD: Highly Optimized Object Oriented Molecular Dynamics
- MDGPU
- LAMMPS GPU Port
- GPUGrid.net
- OpenMM Library for Accelerating Molecular Dynamics on GPUs
- GROMACS using OpenMM
- ACEMD Bio-molecular Dynamics Package
- AMBER CUDA Port
- BigDFT : DFT (Density functional theory) electronic structure code -- Paper PDF
- TeraChem: First Quantum Chemistry Code Written Ground-up for CUDA GPUs
- CUDA Tutorial at Supercomputing ’08 for NAMD and VMD
- NAMD and VMD Publications
- An Implementation of the Smooth Particle-Mesh Ewald (PME) Method on GPU Hardware
- Accelerating AMBER Molecular Dynamic Simulation on GPUs
- HOOMD Publications
- Flourescence Microscopy
- Harvesting Graphics Power for MD Simulations
- Folding @ home (Running GROMACS)
- Ascalaph Liquid MD
GPU Technology Conference Sessions
- Keynote: High-Throughput Science , Hanspeter Pfister, Harvard University
- GPU Accelerated Molecular Dynamics with AMBER, The Scripps Research Institute and San Diego Supercomputer Center
- GPU Accelerated Visualization and Analysis in VMD, University of Illinois at Champaign-Urbana
- Computational Biophysics and Long Range Electrostatics on GPUs, NVIDIA
- Volunteer Computing for GPUs: Petaflops for Free, UC Berkeley
- Harnessing the GPU for Surgical Training and Preoperative Planning, CSIRO
- GPU Accelerated Solvers for ODEs Describing Cardiac Membrane Equations, UC San Diego
- Reconstructing the Brain: Extracting Neural Circuitry with CUDA and MPI, Harvard University
- Unlocking Biologically-Inspired Computer Vision: a High-Throughput Approach, MIT
- A Large Scale Simulation of Lattice QCD with a GPU Cluster, National Taiwan University
- Overview of NVIDIA CUDA Support in AMBER - Lessons Learned, Capabilities Gained, Ross Walker, University of California San Diego, San Diego Supercomputing Center
- Harnessing GPU Speed to Accelerate LAMMPS Particle Simulation, Paul Crozier, Sandia National Laboratory
- Accelerating Molecular Modeling Applications with GPU Computing, John Stone, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign
- Tesla/CUDA Success stories
- Other Tesla Vertical Solutions
- CUDA Software Development Tools & Libraries
