SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)

10.13139/OLCF/1657847

Raw temperature replica-exchange molecular dyanmics trajectories of 23 different SARS CoV-2 Systems including S Protein ACE2-receptor binding-domain, MPro, PLPro, NSP3 ADRP (X-domain/macrodomain/phosphatase), NSP15 (endoribonuclease), NSP9, NSP10, NSP16, and N-protein N-terminus. Systems were prepared with charmm-gui and simulated using the GROMACS simulation software suite. Non-demuxed, i.e. discontinuous/constant temperature window, trajectories are provided in compressed GROMACS xtc and full trr formats. This data supplements the data releases DOI: 10.13139/OLCF/160650 'SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)' and DOI: 10.13139/OLCF/1657844 'SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 2 (Extracted Protein Coordinate Trajectories)'

Published: 2021-01-20 15:01:16 Download Dataset

Dataset Properties

Field Value
Authors
  • Smith, Micholas Dean Oak Ridge National Laboratory
  • Rogers, David Oak Ridge National Laboratory
  • Vermaas, Josh Oak Ridge National Laboratory
  • Smith, Jeremy C Oak Ridge National Laboratory/UTK
Project Identifier BIF128
Dataset Type AS Animations/Simulations
Subjects
  • 59 BASIC BIOLOGICAL SCIENCES
  • 60 APPLIED LIFE SCIENCES
  • 99 GENERAL AND MISCELLANEOUS
Keywords
  • GROMACS
  • SARS-CoV2
  • Molecular Dynamics
  • T-REMD
  • Temperature Replica Exchange
  • COVID-19
Software Needed GROMACS (v2020.1 or greater); VMD (Optional)
Originating Organizations Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);The University of Tennessee, Knoxville, Knoxville, TN (United States)
Sponsoring Organizations Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
DOE Contract DE-AC05-00OR22725
Related Identifiers
  • IsSupplementTo (DOI) 10.13139/OLCF/1650650
  • IsSupplementTo (DOI) 10.13139/OLCF/1657844

Acknowledgements

Papers using this dataset are requested to include the following text in their acknowledgements:

*Support for 10.13139/OLCF/1657847 is provided by the U.S. Department of Energy, project BIF128 under Contract DE-AC05-00OR22725. This research used resources of the Oak Ridge Leadership Computing Facility, which is a DOE Office of Science User Facility.