2.5 Molecular dynamics simulation
Molecular dynamics (MD) simulation of 1 µs was performed for OspA using the Amber18 simulator31 with the AMBER ff14SBonlysc force field31 and the generalized born (GB) solvent model.32 The crystal structure of the protein (PDB:1OSP) was used for the initial conformation. The simulation was conducted with the NVT ensemble, and temperature (350 K) was controlled using a Langevin thermostat with the solvent viscosity of water to 1.0 ps-1. Noncovalent interactions, including electrostatic, van der Waals, and GB, were used without cutoffs. Covalent bonds, including hydrogen atoms, were constrained using the SHAKE method and the integration time step was 2 fs. Snapshots were recorded every 0.1 ns.
Results and Discussion