GALAMOST

Software name: 
GALAMOST
Policy 

HPC2N has a site license, allowing our users to use the program.

General 

GALAMOST is a versatile molecular simulation package which is designed to fully utilize computational power of graphics processing units (GPUs). It is developed specially for coarse-graining simulations of polymeric systems by including some latest techniques.

Description 

GALAMOST is a project of employing high-performance computational techniques to accelerate molecular simulation. At present, the package is developed by fully utilizing the computational power of NVIDIA GPUs. In addition to high-performance computation, a lot of advanced coarse-graining methods and models have been incorporated in this package (listed below). GALAMOST is meant to enable researchers to investigate polymeric systems in a great large temporal and spatial scale, but at a very low cost.

The methods and models incorporated in GALAMOST:

    (1) General molecular dynamics includes Lennard-Jones (LJ), WeeksChandlerAndersen (WCA) potentials and Nosé-Hoover, Berendsen, Andersen thermostats and Andersen, Berendsen barostats etc.
    (2) Dissipative particle dynamics (DPD) is a stochastic simulation technique for simulating the dynamic and rheological properties of simple and complex fluids.
    (3) Brownian dynamics (BD) describes the Langevin dynamics in the motion of particles in solution.
    (4) Coarse-graining molecular dynamics (CGMD) can be implemented by reading the numerical potential derived from iterative Boltzmann inversion (IBI) method which is developed by Müller-Plathe or other structure-based bottom-up coarse-graining methods.
    (5) Reaction model changes 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 describe 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 is 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 is 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 describes the transitional and rotational motion of a rigid body which consists of a group of particles.
    (10) Stretching method imposes a non-equilibrated simulation of extension on polymeric systems to calculate the mechanical properties of materials.

Availability 

On HPC2N we have GALAMOST available as a module on Kebnekaise.

Usage at HPC2N 

GALAMOST is only available on Kebnekaise, since there are no GPUs on Abisko.

To use the GALAMOST module, first add it to your environment. Use:

module spider galamost

to see which versions are available and how to load the module and the needed prerequisites.

Note that while the case does not matter when you use "ml spider", it is necessary to match the case when loading the modules.

Example, loading GALAMOST version 3.0.8

ml GCC/5.4.0-2.26
ml CUDA/8.0.44
ml OpenMPI/2.0.1
ml galamost/3.0.8

You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.

Additional info 

More information about GALAMOST, as well as various documentation, user guides, and examples, can be find on the GALAMOST homepage.

Updated: 2017-12-15, 10:08