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Molecular modeling on GPUs

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Molecular modeling on GPUs

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.

Contents

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.

Programs

  • Abalone – Molecular Dynamics (Benchmark)
  • AMBER on GPUs version
  • Ascalaph on GPUs version – Ascalaph Liquid GPU
  • BigDFT Ab initio program based on wavelet
  • Blaze ligand-based virtual screening
  • 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 version
  • 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
  • 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
  • VMD & NAMD on GPUs versions
  • YASARA runs MD simulations on all GPUs using OpenCL.

    • API

  • 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

    • References

    Molecular modeling on GPUs Wikipedia
    (Text) CC BY-SA