Hoobas: A highly object-oriented builder for molecular dynamics

Martin Girard*, Ali Ehlen, Anisha Shakya, Tristan Bereau, Monica Olvera de la Cruz

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.

Original languageEnglish (US)
Pages (from-to)25-33
Number of pages9
JournalComputational Materials Science
Volume167
DOIs
StatePublished - Sep 2019

Keywords

  • Molecular dynamics
  • Polydispersity
  • Python

ASJC Scopus subject areas

  • Computer Science(all)
  • Chemistry(all)
  • Materials Science(all)
  • Mechanics of Materials
  • Physics and Astronomy(all)
  • Computational Mathematics

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