COVID-19 related trajectory data of 10 microseconds all atom molecular dynamics simulation of SARS-CoV-2 dimeric main protease

Published: 27 Apr 2020 | Version 2 | DOI: 10.17632/vpps4vhryg.2
Contributor(s):

Description of this data

Raw trajectory data (GROMACS format) of 10 microseconds all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease without ligand based on PDB 6LU7, were caclulated on a special purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. We can observe relaxation dynamics and fluctuations of the dimeric protease over the microseconds timescale. We hope that this raw data can help drug development efforts targeting the SARS-CoV-2 main protease. Preparation details and summaries will be submitted to "Data in Brief". More data might be added as new version or another dataset.

Experiment data files

  • Traj1
    Cite

    Single 10 microseconds trajectory of SARS-CoV-2 dimeric main protease, NVT at 310K, with the time step 2.5fs (more precisely, 2.500000409 fs). The starting structure was prepared based on PDB 6LU7, with amber99sb-ildn force field. The system is composed of 98,694 atoms in 9.98921 nm length cubic box with periodic boundary conditions.

    • protein_snap_every200ps
      Cite

      protein snapshots in every 200ps. larger file size.

  • Traj2
    Cite

    Same conditinos with Traj1. Different random seeds for the preparation of solvent and the production run.

Latest version

  • Version 2

    2020-04-27

    Published: 2020-04-27

    DOI: 10.17632/vpps4vhryg.2

    Cite this dataset

    KOMATSU, Teruhisa S.; KOYAMA, Yohei M.; OKIMOTO, Noriaki; MORIMOTO, Gentaro; OHNO, Yousuke; TAIJI, Makoto (2020), “COVID-19 related trajectory data of 10 microseconds all atom molecular dynamics simulation of SARS-CoV-2 dimeric main protease”, Mendeley Data, v2 http://dx.doi.org/10.17632/vpps4vhryg.2

Statistics

Views: 1627
Downloads: 107

Previous versions

Compare to version

Categories

Virus, Drug, Molecular Dynamics

Licence

CC BY 4.0 Learn more

The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.

What does this mean?
You can share, copy and modify this dataset so long as you give appropriate credit, provide a link to the CC BY license, and indicate if changes were made, but you may not do so in a way that suggests the rights holder has endorsed you or your use of the dataset. Note that further permission may be required for any content within the dataset that is identified as belonging to a third party.

Report