Large-Scale Molecular Dynamics Simulations of Cellular Compartments

Eric Wilson, John Vant, Jacob Layton, Ryan Boyd, Hyungro Lee, Matteo Turilli, Benjamín Hernández, Sean Wilkinson, Shantenu Jha, Chitrak Gupta, Daipayan Sarkar, Abhishek Singharoy

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages22
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Ensemble toolkit
  • High-performance computing
  • Molecular dynamics
  • Multiscale simulation
  • NAMD
  • Photosynthetic chromatophore
  • VMD

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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