David J. Hardy, John E. Stone, Barry Isralewitz, and Emad Tajkhorshid.
Lessons learned from responsive molecular dynamics studies of the
COVID-19 virus.
IEEE/ACM HPC for Urgent Decision Making 2021, pp. 1-10,
2021.
HARD2021-ET
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.
