Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus

David J. Hardy, John E. Stone, Barry Isralewitz, Emad Tajkhorshid

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation software, and the necessary computing resources to conduct their work. We describe our experiences from several COVID-19 research collaborations and the challenges they presented in terms of our molecular modeling software development and support efforts, our laboratory's local computing environment, and our scientists' use of non-traditional HPC hardware platforms such as public clouds for large scale parallel molecular dynamics simulations.

Original languageEnglish (US)
Title of host publicationProceedings of UrgentHPC 2021
Subtitle of host publication3rd International Workshop on HPC for Urgent Decision Making, Held in conjunction with SC 2021: The International Conference for High Performance Computing, Networking, Storage and Analysis
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1-10
Number of pages10
ISBN (Electronic)9781665411301
DOIs
StatePublished - 2021
Event3rd IEEE/ACM International Workshop on HPC for Urgent Decision Making, UrgentHPC 2021 - St. Louis, United States
Duration: Nov 19 2021 → …

Publication series

NameProceedings of UrgentHPC 2021: 3rd International Workshop on HPC for Urgent Decision Making, Held in conjunction with SC 2021: The International Conference for High Performance Computing, Networking, Storage and Analysis

Conference

Conference3rd IEEE/ACM International Workshop on HPC for Urgent Decision Making, UrgentHPC 2021
Country/TerritoryUnited States
CitySt. Louis
Period11/19/21 → …

Keywords

  • COVID-19
  • Interactive Computing
  • Molecular Dynamics Simulation
  • Remote Visualization
  • SARS-CoV-2

ASJC Scopus subject areas

  • Computer Science Applications
  • Decision Sciences (miscellaneous)
  • Information Systems and Management
  • Statistics, Probability and Uncertainty

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