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

    Micholas Dean Smith | Oak Ridge National Laboratory
    David Rogers | Oak Ridge National Laboratory
    Josh Vermaas | Oak Ridge National Laboratory
    Jeremy C Smith | Oak Ridge National Laboratory/UTK
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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 Information

DOE Contract Number

DE-AC05-00OR22725

Originating 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)

Project Identifier

BIF128

Related Works

Details

DOI

https://doi.org/10.13139/OLCF/1657847

Release Date

January 20, 2021

Subject

BASIC BIOLOGICAL SCIENCES, APPLIED LIFE SCIENCES, GENERAL AND MISCELLANEOUS

Keywords

GROMACS, SARS-CoV2, Molecular Dynamics, T-REMD, Temperature Replica Exchange, COVID-19

Dataset

Dataset Type

AS Animations/Simulations

Software

GROMACS (v2020.1 or greater); VMD (Optional)

Cite This Dataset:

Smith, M., Rogers, D., Vermaas, J., Smith, J. (2021). SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 3 (Raw Temperature Replica Exchange Molecular Dynamics Trajectories). Oak Ridge National Laboratory. https://doi.org/10.13139/OLCF/1657847.

Acknowledgements

This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Advanced Scientific Computing Research programs in the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.