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GPU Applications

Molecular Dynamics

Molecular dynamics applications are extremely amenable to the massively parallel architecture of NVIDIA's GPUs. In the charts below, we highlight work done on VMD and also molecular dynamics software packages such as NAMD and HOOMD.

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Molecular Dynamics Ion Placement VMD

Generalized Born simulation in AMBER
San Diego Supercomputing Center

Molecular Dynamics Lennard Jones

Scaling of NAMD on a GPU-cluster
Theoretical and Computational Bio-physics Group, UIUC

Other Relevant Software Using CUDA
> HOOMD: Highly Optimized Object Oriented Molecular Dynamics
> LAMMPS GPU Port
> GPUGrid.net
> OpenMM Library for Accelerating Molecular Dynamics on GPUs
> ACEMD Bio-molecular Dynamics Package
> BigDFT : DFT (Density functional theory) electronic structure code -- Paper PDF
> TeraChem: First Quantum Chemistry Code Written Ground-up for CUDA GPUs
 
Technical Reports on Molecular Dynamics on CUDA
> Accelerating VASP: Speeding up plane-wave electronic-structure calculations using graphics-processing units
> 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)
> Todd Martinez work on Quantum Chemistry on GPUs
> Q-Chem on CUDA
> NAMD and VMD Publications

CUDA-Acceleration in Related Verticals
> Computational Chemistry
> Medical Imaging
> Bio-informatics and Life Sciences
> ArrayFire GPU function library for C, C++, FORTRAN
> MATLAB®
 
See Also
> Tesla/CUDA Success stories
> Other Tesla Vertical Solutions
> CUDA Software Development Tools & Libraries
> Buy Tesla