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.

With the introduction of NVIDIA Tesla Bio Workbench, it provides bio-physicists and computational chemists the tools to push the boundaries of bio-chemical research, optimizing the scientific workflow and accelerating the pace of research. Learn more.

Generalized Born simulation in AMBER San Diego Supercomputing Center	Scaling of NAMD on a GPU-cluster Theoretical and Computational Bio-physics Group, UIUC

* Expected Speed Up vs a quad-core x64 CPU based system. Speed-ups as per NVIDIA in house testing or application provider documentation.

• 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

• Accelerating VASP: Speeding up plane-wave electronic-structure calculations using graphics-processing units
• 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

• 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

• Computational Chemistry
• Medical Imaging
• Bio-informatics and Life Sciences
• MATLAB acceleration

• Other Tesla Vertical Solutions
• CUDA Software Development Tools & Libraries