Molecular modeling on GPU is the technique of using a
graphics processing unit
A graphics processing unit (GPU) is a specialized electronic circuit designed to manipulate and alter memory to accelerate the creation of images in a frame buffer intended for output to a display device. GPUs are used in embedded systems, m ...
(GPU) for
molecular simulations.
In 2007,
NVIDIA
Nvidia CorporationOfficially written as NVIDIA and stylized in its logo as VIDIA with the lowercase "n" the same height as the uppercase "VIDIA"; formerly stylized as VIDIA with a large italicized lowercase "n" on products from the mid 1990s to ...
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
An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how ...
(API) named
CUDA
CUDA (or Compute Unified Device Architecture) is a parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for general purpose processing, an approach ...
. This technology substantially simplified programming by enabling programs to be written in
C/
C++
C++ (pronounced "C plus plus") is a high-level general-purpose programming language created by Danish computer scientist Bjarne Stroustrup as an extension of the C programming language, or "C with Classes". The language has expanded significan ...
. More recently,
OpenCL
OpenCL (Open Computing Language) is a software framework, framework for writing programs that execute across heterogeneous computing, heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), d ...
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
Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions ...
calculations and
molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...
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 classi ...
) 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
Abalone ( or ; via Spanish , from Rumsen ''aulón'') is a common name for any of a group of small to very large marine gastropod molluscs in the family Haliotidae. Other common names are ear shells, sea ears, and, rarely, muttonfish or mutto ...
– Molecular Dynamics
Benchmark
*
ACEMD on GPUs sinc
2009Benchmark
*AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In M ...
on GPU
version
on GPUs version �
*AutoDock
AutoDock is a molecular modeling simulation software. It is especially effective for protein-ligand docking. AutoDock 4 is available under the GNU General Public License. AutoDock is one of the most cited docking software applications in the re ...
– Molecular docking
* BigDFT ''Ab initio'' program based on wavelet
A wavelet is a wave-like oscillation with an amplitude that begins at zero, increases or decreases, and then returns to zero one or more times. Wavelets are termed a "brief oscillation". A taxonomy of wavelets has been established, based on the num ...
BrianQC
Quantum chemistry ( HF and DFT) and molecular mechanics
Blaze
ligand-based virtual screening
*CP2K
CP2K is a freely available ( GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It prov ...
Ab initio molecular dynamics
*Desmond (software)
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical methods to achieve ...
on GPUs, workstations, and clusters
*Firefly
The Lampyridae are a family of elateroid beetles with more than 2,000 described species, many of which are light-emitting. They are soft-bodied beetles commonly called fireflies, lightning bugs, or glowworms for their conspicuous production ...
(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
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source softw ...
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
TeraChem is a computational chemistry software program designed for CUDA-enabled Nvidia GPUs. The initial development started at the University of Illinois at Urbana-Champaign and was subsequently commercialized. It is currently distributed by Pet ...
– Quantum chemistry and ''ab initio'' Molecular Dynamics
*TINKER
Tinker or tinkerer is an archaic term for an itinerant tinsmith who mends household utensils.
Description
''Tinker'' for metal-worker is attested from the thirteenth century as ''tyckner'' or ''tinkler''. Some travelling groups and Romani p ...
on GPUs.
versions
* YASARA runs MD simulations on all GPUs using OpenCL
OpenCL (Open Computing Language) is a software framework, framework for writing programs that execute across heterogeneous computing, heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), d ...
.
API
BrianQC
– has an open C level API for quantum chemistry simulations on GPUs, provides GPU-accelerated version of Q-Chem
Q-Chem is a general-purpose electronic structure package featuring a variety of established and new methods implemented using innovative algorithms that enable fast calculations of large systems on various computer architectures, from laptops and ...
and PSI
OpenMM
– an API for accelerating molecular dynamics on GPUs, v1.0 provides GPU-accelerated version of GROMACS
mdcore
– an open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized so ...
platform-independent library for molecular dynamics simulations on modern shared-memory
In computer science, shared memory is memory that may be simultaneously accessed by multiple programs with an intent to provide communication among them or avoid redundant copies. Shared memory is an efficient means of passing data between prog ...
parallel architectures.
Distributed computing projects
GPUGRID
distributed supercomputing infrastructure
*Folding@home
Folding@home (FAH or F@h) is a volunteer computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements ...
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