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