Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling

DOI10.4208/cicp.OA-2022-0046MaRDI QIDQ5887618

Fabio Bonaccorso, Adriano Tiribocchi, Alessandro Loppini, Simonetta Filippi, Mihir Durve, Unnamed Author, Sauro Succi, Marco Lauricella, Andrea Montessori

Publication date: 13 April 2023

Published in: Communications in Computational Physics (Search for Journal in Brave)

zbMATH Keywords

molecular dynamicsbiophysicslattice BoltzmannSARS-CoV-2

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biophysics (92C05) Physiological flow (92C35) Boltzmann equations (35Q20) Computational molecular dynamics in statistical mechanics (82M37)

Related Items

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Uses Software

• Gromacs
• PDB2PQR
• I-TASSER
• VMD

Cites Work

• Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid
• Fast parallel algorithms for short-range molecular dynamics
• Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces
• The Lattice Boltzmann Equation
• Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore