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Molecular modeling on GPU

Molecular modeling on GPU

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Molecular modeling on GPU is the technique of using a graphics processing unit
Graphics processing unit
A graphics processing unit or GPU is a specialized circuit designed to rapidly manipulate and alter memory in such a way so as to accelerate the building of images in a frame buffer intended for output to a display...

 (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 (currently up to 512) working in parallel. Long before this event, the computational power of video cards was used to accelerate calculations. What was new is that stream processing
Stream processing
Stream processing is a computer programming paradigm, related to SIMD , that allows some applications to more easily exploit a limited form of parallel processing...

 made it possible to develop parallel programs in a high-level language. This technology substantially simplified programming by enabling programs to be written in C/C++.

Quantum chemistry
Quantum chemistry
Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems...

 calculations

and molecular mechanics
Molecular mechanics
Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

 simulations
(molecular modeling in terms of classical mechanics
Classical mechanics
In physics, classical mechanics is one of the two major sub-fields of mechanics, which is concerned with the set of physical laws describing the motion of bodies under the action of a system of forces...

) are among beneficial applications of this technology. The video cards can accelerate the calculations tens of times. Thus, a PC with such a card has the power similar to that of a cluster of workstations based on the common processors.

See also



Programs

  • Abalone
    Abalone (molecular mechanics)
    Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit water or in implicit water models...

  • AceMD the biomolecular MD package used by GPUGRID
  • AMBER
    AMBER
    AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...

     on GPUs version
  • Ascalaph on GPUs version – Ascalaph Liquid GPU
  • BigDFT Ab initio program based on wavelet
    Wavelet
    A wavelet is a wave-like oscillation with an amplitude that starts out at zero, increases, and then decreases back to zero. It can typically be visualized as a "brief oscillation" like one might see recorded by a seismograph or heart monitor. Generally, wavelets are purposefully crafted to have...

  • GPIUTMD – Graphical processors for Many-Particle Dynamics
  • GROMACS on GPUs version
  • HALMD – Highly Accelerated Large-scale MD package
  • HOOMD – Highly Optimized Object Oriented Molecular Dynamics
  • LAMMPS
    LAMMPS
    LAMMPS is a molecular dynamics program from Sandia National Laboratories.. LAMMPS makes use of MPI for parallel communication and is a free open-source code, distributed under the terms of the GNU General Public License.LAMMPS was originally developed under a Cooperative Research and Development...

     on GPUs version – gpulammps
  • TeraChem
    TeraChem
    TeraChem is the first computational chemistry software program written completely from scratch to benefit from the new streaming processors such as Graphics Processing Units . The computational algorithms have been completely redesigned to exploit massive parallelism of CUDA-enabled NVIDIA GPUs...

     - Quantum chemistry and ab initio Molecular Dynamics
  • VMD
    Visual Molecular Dynamics
    - External links :* * *...

     & NAMD
    NAMD
    NAMD is a free-of-charge molecular dynamics simulation package written using the Charm++ parallel programming model, noted for its parallel efficiency and often used to simulate large systems...

    on GPUs versions

API

  • OpenMM – an API for accelerating molecular dynamics on GPUs, v1.0 provides GPU-accelerated version of GROMACS

Distributed computing projects