COVID-19 related trajectory data of 10 microseconds all atom molecular dynamics simulation of SARS-CoV-2 dimeric main protease
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
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 snapshots in every 200ps. larger file size.
Same conditinos with Traj1. Different random seeds for the preparation of solvent and the production run.
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
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The files associated with this dataset are licensed under a Creative Commons Attribution 4.0 International licence.