Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.^[1]

In 2007,

• Abalone – Molecular Dynamics (Benchmark)
• ACEMD on GPUs since 2009 Benchmark
• AMBER on GPUs version
• Ascalaph on GPUs version – Ascalaph Liquid GPU
• AutoDock – Molecular docking
• BigDFT Ab initio program based on wavelet
• BrianQC Quantum chemistry (HF and DFT) and molecular mechanics
• Blaze ligand-based virtual screening
• CHARMM – Molecular dynamics [1]
• CP2K Ab initio molecular dynamics
• Desmond (software) on GPUs, workstations, and clusters
• Firefly (formerly PC GAMESS)
• FastROCS
• GOMC – GPU Optimized Monte Carlo simulation engine
• GPIUTMD – Graphical processors for Many-Particle Dynamics
• GPUMD - A light weight general-purpose molecular dynamics code
• GROMACS on GPUs ^[11]
• HALMD – Highly Accelerated Large-scale MD package
• HOOMD-blue Archived 2011-11-11 at the Wayback Machine – Highly Optimized Object-oriented Many-particle Dynamics—Blue Edition
• LAMMPS on GPUs version – lammps for accelerators
• LIO DFT-Based GPU optimized code - [2]
• Octopus has support for OpenCL.
• oxDNA – DNA and RNA coarse-grained simulations on GPUs
• PWmat – Plane-Wave Density Functional Theory simulations
• RUMD - Roskilde University Molecular Dynamics^[12]
• TeraChem – Quantum chemistry and ab initio Molecular Dynamics
• TINKER on GPUs.^[13]
• VMD & NAMD on GPUs versions
• YASARA runs MD simulations on all GPUs using OpenCL.

API

• BrianQC – has an open C level API for quantum chemistry simulations on GPUs, provides GPU-accelerated version of Q-Chem and PSI
• OpenMM – an API for accelerating molecular dynamics on GPUs, v1.0 provides GPU-accelerated version of GROMACS
• mdcore – an
  shared-memory
  parallel architectures.

Distributed computing projects

• GPUGRID distributed supercomputing infrastructure
• Folding@home distributed computing project

See also

References