Molecular modeling on GPU is the technique of using a graphics processing unit (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 (, 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.
GPU accelerated molecular modelling software
Programs
Abalone – Molecular Dynamics (Benchmark) ACEMD on GPUs since 2009 Benchmark AMBER on GPUs version Ascalaph on GPUs version – Ascalaph Liquid GPU AutoDock – Molecular docking BigDFT Ab initio program based on wavelet BrianQC Quantum chemistry (HF and DFT) and molecular mechanics Blaze ligand-based virtual screening CHARMM – Molecular dynamics CP2K Ab initio molecular dynamics 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 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 accelerators LIO DFT-Based GPU optimized code - 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. VMD & NAMD 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.