Molecular modeling on GPU is the technique of using a

graphics processing unit A graphics processing unit (GPU) is a specialized electronic circuit designed for digital image processing and to accelerate computer graphics, being present either as a discrete video card or embedded on motherboards, mobile phones, personal ...

(GPU) for molecular simulations. In 2007,

Nvidia Nvidia Corporation ( ) is an American multinational corporation and technology company headquartered in Santa Clara, California, and incorporated in Delaware. Founded in 1993 by Jensen Huang (president and CEO), Chris Malachowsky, and Curti ...

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. The new features of these cards made it possible to develop parallel programs in a high-level

application programming interface An application programming interface (API) is a connection between computers or between computer programs. It is a type of software Interface (computing), interface, offering a service to other pieces of software. A document or standard that des ...

(API) named

CUDA In computing, CUDA (Compute Unified Device Architecture) is a proprietary parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for accelerated gene ...

. This technology substantially simplified programming by enabling programs to be written in C/ C++. 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), di ...

allows

cross-platform Within 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 platform, computing platforms. Some ...

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 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 scienc ...

in terms of

classical mechanics Classical mechanics is a Theoretical physics, physical theory describing the motion of objects such as projectiles, parts of Machine (mechanical), machinery, spacecraft, planets, stars, and galaxies. The development of classical mechanics inv ...

) 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 language, Rumsen ''aulón'') is a common name for any small to very large marine life, marine gastropod mollusc in the family (biology), family Haliotidae, which once contained six genera but now cont ...

– Molecular Dynamics
Benchmark
* ACEMD on GPUs sinc
2009Benchmark
*

AMBER Amber is fossilized tree resin. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia ...

on GPU
version
on GPUs version �

* AutoDock – Molecular docking *

BigDFT BigDFT is a free software package for physicists and chemists, distributed under the GNU General Public License, whose main program allows the total energy, charge density, and electronic structure of systems made of electrons and nuclei (mole ...

''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 n ...

BrianQC
Quantum chemistry ( HF and DFT) and molecular mechanics
Blaze
ligand-based virtual screening *

CHARMM Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CH ...

– Molecular dynamic

*

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
GPU4PySCF
– GPU accelerated plugin package fo
PySCFGPUMD
- A light weight general-purpose molecular dynamics code *

GROMACS GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors ...

on GPUs
HALMD
– Highly Accelerated Large-scale MD package
HOOMD-blue
– Highly Optimized Object-oriented Many-particle Dynamics—Blue Edition *

LAMMPS LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular dynamics program developed by Sandia National Laboratories. It utilizes the Message Passing Interface (MPI) for parallel communication, enabling high-performance s ...

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 Peta ...

– Quantum chemistry and ''ab initio'' Molecular Dynamics *

TINKER Tinker or tinkerer is an archaic term for an wikt:itinerant, itinerant tinsmith who mends household utensils. Description ''Tinker'' for metal-worker is attested from the thirteenth century as ''tyckner'' or ''tinkler''. Some travelling grou ...

on GPUs. * VMD & NAMD on GPU
versions
* YASARA runs MD simulations on all GPUs using

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 Psi, PSI or Ψ may refer to: Alphabetic letters * Psi (Greek) (Ψ or ψ), the twenty-third letter of the Greek alphabet * Psi (Cyrillic), letter of the early Cyrillic alphabet, adopted from Greek Arts and entertainment * "Psi" as an abbreviat ...

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 and view the source code, design documents, or content of the product. The open source model is a decentrali ...

platform-independent library for molecular dynamics simulations on modern shared-memory parallel architectures.

Distributed computing projects

GPUGRID
distributed supercomputing infrastructure *

Folding@home Folding@home (FAH or F@h) is a distributed 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 * Exscalate4Cov large-scale virtual screening experiment

References

External links

More links for classical and quantum сhemistry on GPUs
{{Processor technologies Molecular modelling Computational chemistry Molecular dynamics Chemistry software GPGPU

GPU accelerated molecular modelling software

Programs

API

Distributed computing projects

See also

References

External links