Overview
HOOMD stands for Highly Optimized Object Oriented Molecular Dynamics. It performs general purpose molecular dynamics simulations on a single workstation, taking advantage of the NVIDIA GPUs to attain a level of performance equivalent to roughly dozens of processor cores on a fast cluster.
The object oriented design of HOOMD makes it versatile and expandable. A number of different force fields and integrators are present in the current version, and additional ones can be added easily.
Simulations are setup and run using very simple python scripts, allowing complete control over the force field, integrator, all parameters, how many time steps are run, and so on. The scripting system is designed to be as simple as possible to the non-programmer.
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Paper
The algorithms and implementation of HOOMD are discussed in the paper:
General purpose molecular dynamics simulations fully implemented on graphics processing units
Joshua A. Anderson, Chris D. Lorenz, and Alex Travesset
Journal of Computational Physics 227 (2008) 5342-5359
DOI: 10.1016/j.jcp.2008.01.047
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Features
- Executes Molecular Dynamics on NVIDIA GPUs with the same performance as a small cluster of CPUs
- Supports Windows, Linux, and Mac OS X
- Pair Potentials
- Lennard-Jones
- Bond Potentials
- FENE
- Harmonic
- Wall Potentials
- Lennard-Jones
- Integrators
- Brownian dynamics NVT
- NPT
- NVE
- NVT
- Dump file formats
- HOOMD's XML input format
- MOL2
- DCD
- Large simulations can be run on multiple GPUs in a single host
- Simple but powerful script interface for defining simulations
- Advanced built-in initial configuration generators
- Human readable XML input files
- Space-filling curve particle reordering to increase performance
- Extensible object-oriented design, so adding additional potentials and integrators is straightforward.
- Simulations can be visualized in real-time using VMD's IMD interface.
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