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

Learn more about Molecular Dynamic codes by downloading the Life Science Apps Catalog

• HOOMD: Highly Optimized Object Oriented Molecular Dynamics
• MDGPU
• 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
• 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
• Todd Martinez work on Quantum Chemistry on GPUs
• Q-Chem on CUDA
• NAMD and VMD Publications
• Molecular Dynamics on a GPU Grid

• Towards Routine Microsecond Molecular Dynamics Simulations on Commodity Hardware-University of California San Diego
• GPU-Accelerated Molecular Dynamics Simulations of Solid Covalent Crystals– Chinese Academy of Sciences
• Advancing GPU Molecular Dynamics: Rigid Bodies in HOOMD-blue– Joshua Anderson
• An Innovative Massively Parallelized Molecular Dynamic Software– IFPEN
• Compuational Screening of Novel Carbon Capture Materials– UC Berkeley/Berkely Lab
• Petascale Molecular Dynamics Simulations on GPU-Accelerated Supercomputers– University of Illinois at Urbana-Champaign
• GPU-Based Molecular Dynamics Simulations of Protein and RNA Assembly– Wake Forest University
• VMD: High Performance Molecular Visualization and Analysis on GPUs– University of Illinois at Urbana-Champaign
• A Study of Persistent Threads Style Programming Model for GPU Computing– UC Davis
• Terascale Volume Visualization in Neuroscience- KAUST
• GPU Enabled Macromolecular Simulation: Challenges and Opportunities– University of Delaware
• Probing Bio-Nano Interface Structure from Microsecond Molecular Dynamics on GPUs– Case Western Reserve University
• Strong Scaling for Molecular Dynamics Applications– NVIDIA
• Efficient Molecular Dynamics on Heterogeneous GPU Architectures in GROMACS– KTH Royal Institute of Technology
• Molecule Dynamics, GPUs, and EC2– Amazon Web Services

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