SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories)
- 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
Overview
Description
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)'
Funding resources
DOE contract number
DE-AC05-00OR22725Originating research organization
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States);The University of Tennessee, Knoxville, Knoxville, TN (United States)Sponsoring organization
Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)Related resources
- IsSupplementTo (DOI): https://doi.org/10.13139/OLCF/1650650
- IsSupplementTo (DOI): https://doi.org/10.13139/OLCF/1657844
Details
DOI
10.13139/OLCF/1657847Release date
January 20, 2021Dataset
Dataset type
AS Animations/SimulationsSoftware
GROMACS (v2020.1 or greater); VMD (Optional)Acknowledgements
Users should acknowledge the OLCF in all publications and presentations that speak to work performed on OLCF resources:
This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.
Category
- 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