GPU-Accelerated Large-Scale Molecular Simulation Toolkit
Station: Introduction
GALAMOST is a package of employing high-performance computational techniques on many-core processors to accelerate molecular dynamics simulations. At present, the package is written with CUDA and C++ languages for particularly running on NVIDIA GPUs. This package focuses on the large scale simulations of soft matters. The package is developed and maintained by Dr. You-Liang Zhu under the guidance of Prof. Zhong-Yuan Lu and Prof. Zhao-Yan Sun. In addition to high-performance computations, many advanced coarse-graining methods and models have been incorporated in this package (some of them listed below). By the boost of GPU, GALAMOST could enable researchers to investigate soft matter systems in a great large temporal and spatial scale, while at a very low cost.

The methods and models incorporated in GALAMOST:

(1) General molecular dynamics: including Lennard-Jones (LJ), WeeksChandlerAndersen (WCA) potentials and Nosé-Hoover, Berendsen, Andersen thermostats and Andersen, Berendsen barostats etc.
(2) Dissipative particle dynamics (DPD): a stochastic simulation technique for simulating the dynamic and rheological properties of simple and complex fluids.
(3) Brownian dynamics (BD): describing the Langevin dynamics in the motion of particles in solution.
(4) Coarse-graining molecular dynamics (CGMD): which is implemented by reading the numerical potentials derived from iterative Boltzmann inversion (IBI) method developed by Müller-Plathe, reverse Monte Carlo (RMC) developed by Aatto Laaksonen, or other structure-based bottom-up coarse-graining methods.
(5) Reaction model: changing the topological connections between particles according to certain probability which is derived from real reaction rates. This model which is developed by Hong Liu can be applied to the chain-growth polymerization, step-growth polymerization, "Graft to" polymerization, polymeric ligand exchanged, the molecular mobility of polymeric graft, and so on.
(6) Anisotropic particle models: describing the rigid ellipsoidal particles by Gay-Berne model and describe the soft patchy particles by a soft anisotropic particle developed by Zhan-Wei Li.
(7) MD-SCF: a hybrid particle-field molecular dynamics technique which combines the self-consistent field (SCF) theory and molecular dynamics (MD). It is developed by Giuseppe Millano. It will largely speed up some slowly evolving collective processes in MD simulations, such as microphase separation and self-assembly of polymeric systems.
(8) DNA 3SPN model: a coarse-grained three-site-per-nucleotide model of DNA and reduce the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base.
(9) Rigid body method: describing the transitional and rotational motion of a rigid body which consists of a group of particles.
(10) Stretching method: imposing a non-equilibrated simulation of extension on polymeric systems to calculate the mechanical properties of materials.