Atomic Resolution Brownian Dynamics

GPU-accelerated Brownian dynamics simulation tool for biomolecular and nanotechnological systems

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Version 1.0a - published on 29 Nov 2016

doi:10.4231/D3736M35T cite this

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Abstract

Brownian dynamics (BD) simulation is method for studying biomolecules, ions, and nanomaterials that balances detail with computational efficiency.

ARBD supports tabulated non-bonded and bonded interactions between BD particles that can also be influenced by grid-specified potentials. Uniquely, ARBD also allows grid-specified densities and potentials to be associated with rigid body particles that rotate and translate to represent larger molecules. Most importantly, the code is designed to run quickly on modern NVIDIA GPUs.
 

Cite this work

Researchers should cite this work as follows:

  • "Atoms-to-microns model for small solute transport through sticky nanochannels"
    Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev
    Lab Chip 11(22) 3766-73 (2011)
     

  • Chris Maffeo (2016), "Atomic Resolution Brownian Dynamics," https://nanohub.org/resources/arbd. (DOI: 10.4231/D3736M35T).

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Tags

  1. brownian dynamics
  2. CUDA
  3. GPU
  4. nano/bio
  5. polymers
  6. rigid body
  7. Simulation