Ionic liquid simulation on GPU (Abalone)
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
In 2007, NVIDIA
introduced video cards that could be used not only to show graphics but
also for scientific calculations. These cards include many arithmetic
units (as of 2016, up to 3,584 in Tesla P100) working in parallel. Long
before this event, the computational power of video cards was purely
used to accelerate graphics calculations. What was new is that NVIDIA
made it possible to develop parallel programs in a high-level application programming interface (API) named CUDA. This technology substantially simplified programming by enabling programs to be written in C/C++. More recently, OpenCL allows cross-platform GPU acceleration.
Quantum chemistry calculations and molecular mechanics simulations (molecular modeling in terms of classical mechanics)
are among beneficial applications of this technology. The video cards
can accelerate the calculations tens of times, so a PC with such a card
has the power similar to that of a cluster of workstations based on
common processors.
GPU accelerated molecular modelling software
Programs
- Abalone – Molecular Dynamics (Benchmark)
- ACEMD on GPUs since 2009 Benchmark
- AMBER on GPUs version
- Ascalaph on GPUs version – Ascalaph Liquid GPU
- BigDFT Ab initio program based on wavelet
- BrianQC Quantum chemistry (HF and DFT) and molecular mechanics
- Blaze ligand-based virtual screening
- 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
- GROMACS on GPUs
- HALMD – Highly Accelerated Large-scale MD package
- HOOMD-blue – Highly Optimized Object-oriented Many-particle Dynamics—Blue Edition
- LAMMPS on GPUs version – lammps for accelerators
- LIO DFT-Based GPU optimized code
- Octopus has support for OpenCL.
- oxDNA – DNA and RNA coarse-grained simulations on GPUs
- PWmat – Plane-Wave Density Functional Theory simulations
- TeraChem – Quantum chemistry and ab initio Molecular Dynamics
- TINKER on GPUs.
- 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
- OpenMM – an API for accelerating molecular dynamics on GPUs, v1.0 provides GPU-accelerated version of GROMACS
- mdcore – an open-source platform-independent library for molecular dynamics simulations on modern shared-memory parallel architectures.
Distributed computing projects
- GPUGRID distributed supercomputing infrastructure
- Folding@home distributed computing project
