Molecular modeling on GPU is the technique of using a
graphics processing unit (GPU) for
molecular simulations
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials sc ...
.
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 (, 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
In computing, cross-platform software (also called multi-platform software, platform-agnostic software, or platform-independent software) is computer software that is designed to work in several computing platforms. Some cross-platform software ...
GPU acceleration.
Quantum chemistry calculations and
molecular mechanics simulations (
molecular modeling in terms of
classical mechanics
Classical mechanics is a physical theory describing the motion of macroscopic objects, from projectiles to parts of machinery, and astronomical objects, such as spacecraft, planets, stars, and galaxies. For objects governed by classical ...
) 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 sinc
2009Benchmark
* AMBER on GPU
version
on GPUs version �
* AutoDock – Molecular docking
* 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)
FastROCSGOMC
– 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
HALMD
– Highly Accelerated Large-scale MD package
HOOMD-blue
– Highly Optimized Object-oriented Many-particle Dynamics—Blue Edition
* LAMMPS on GPUs version �
lammps for acceleratorsLIO
DFT-Based GPU optimized code
* Octopus (software), 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
* TeraChem – Quantum chemistry and ''ab initio'' Molecular Dynamics
* TINKER 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 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
See also
References
External links
More links for classical and quantum сhemistry on GPUs
{{Processor technologies
Molecular modelling
Computational chemistry
Molecular dynamics
Chemistry software
GPGPU