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Name: Gromacs 60 ns MD of SARS-CoV-2 spike trimer, All Atom model (60 ns)
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6VXX
Description: This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The proteinwas solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performedwith Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
Extracted from: BioExcel (ID: MCV1900064)
Author: Dmitry Morozov
Submission date: October 22, 2020
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 52329
Simulation details
Software and version: GROMACS 2018.8
Forcefield and version: charmm27
Time step : 2.0 fs
Delta : 0.08 ns
Replicates: 1
Accumulated simulation time: 0.0578 µs
References
SARS-CoV-2 Spike Protein Model for Computational Screening of Therapeutic COVID-19 Drugs. Dmitry Morozov1, Gerrit Groenhof1, Vladimir Mironov2
1. Department of Chemistry and Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
2. Chemistry Department, Moscow State University, 119991 Moscow, Russia
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