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Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.

Karina van den Broek1,2, Hubert Kuhn3, Achim Zielesny4

  • 1Inorganic Chemistry and Center for Nanointegration, University of Duisburg-Essen, Essen, Germany.

Journal of Cheminformatics
|May 23, 2018
PubMed
Summary
This summary is machine-generated.

Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics. This tool offers parallelizable force calculations and efficient caching for faster molecular simulations.

Keywords:
Dissipative particle dynamicsKernelMesoscopicMolecularSimulation

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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • Software Engineering

Background:

  • Molecular Fragment Dissipative Particle Dynamics (MF-DPD) is a coarse-grained simulation method.
  • Existing simulation kernels may present challenges in terms of flexibility and polyglot programming.

Purpose of the Study:

  • Introduce Jdpd, a novel open Java simulation kernel for MF-DPD.
  • Enhance the efficiency and usability of MF-DPD simulations.

Main Methods:

  • Developed an open Java simulation kernel (Jdpd).
  • Implemented parallelizable force calculations.
  • Incorporated efficient caching and fast property calculations.
  • Designed with an interface and factory-pattern for code flexibility.

Main Results:

  • Jdpd provides parallelizable force calculations.
  • Features efficient caching and fast property calculations.
  • The design facilitates simple code modifications and avoids polyglot programming issues.
  • Supports detailed I/O, parallelization, process control, and internal logging.

Conclusions:

  • Jdpd offers a flexible and efficient kernel for MF-DPD simulations.
  • The design promotes ease of use and integration into various simulation environments.
  • Suitable for scripting solutions and integrated simulation systems.