Jdpd

Jdpd is a tool to simulate Molecular Fragment Dissipative Particle Dynamics (DPD). The Jdpd algorithm uses parallelizable force calculation, rapid property computation and includes efficient caching.

Topic

Cheminformatics;Molecular dynamics;Structure analysis;Simulation experiment

Detail

  • Operation: Molecular dynamics

  • Software interface: Graphical user interface

  • Language: Java

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.6.0.0

  • Credit: Gesellschaft für naturwissenschaftliche Informatik mbH GNWI.

  • Input: -

  • Output: -

  • Contact: Karina van den Broek karina.broek@studmail.w-hs.de, Hubert Kuhn kuhn@molecular-dynamics.de, Achim Zielesny achim.zielesny@w-hs.de

  • Collection: -

  • Maturity: Stable

Publications

  • Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation
  • van den Broek K, Epple M, Kersten LS, Kuhn H, Zielesny A. Quantitative Estimation of Cyclotide-Induced Bilayer Membrane Disruption by Lipid Extraction with Mesoscopic Simulation. J Chem Inf Model. 2021 Jun 28;61(6):3027-3040. doi: 10.1021/acs.jcim.1c00332. Epub 2021 May 19. PMID: 34008405.
  • https://doi.org/10.1021/acs.jcim.1c00332
  • PMID: 34008405
  • PMC: -
  • Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics.
  • van den Broek K, Kuhn H, Zielesny A. Jdpd: an open java simulation kernel for molecular fragment dissipative particle dynamics. J Cheminform. 2018 May 21;10(1):25. doi: 10.1186/s13321-018-0278-7. PMID: 29785513; PMCID: PMC5962482.
  • https://doi.org/10.1186/s13321-018-0278-7
  • PMID: 29785513
  • PMC: PMC5962482

Download and documentation

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