Trajectory data of molecular dynamics simulation of SARS-CoV-2 Main Protease and inhibitor drug candidates

Published: 21 April 2020| Version 2 | DOI: 10.17632/5jfsx6j75g.2
Ryunosuke Yoshino, Nobuaki Yasuo,


MD simulations were performed using Desmond on supercomputer TSUBAME 3.0. The inhibitor-SARS-CoV-2 Mpro complex models were placed in the orthorhombic box with a buffer distance of 10 Å in order to create a hydration model. TIP3P water model was used for creation of the hydration model. We performed MD simulations under the NPT ensemble for 1 μs on three complex structures using OPLS3e force field.



Drug, Molecular Dynamics, Molecular Docking, Severe Acute Respiratory Syndrome Coronavirus 2, Coronavirus Disease 2019