Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step

Abstract

Recently, we proposed novel temperature and pressure evaluations in molecular dynamics (MD) simulations to preserve the accuracy up to the third order of a time step, δt [J. Jung, C. Kobayashi, and Y. Sugita, J. Chem. Theory Comput. 15, 84-94 (2019); J. Jung, C. Kobayashi, and Y. Sugita, J. Chem. Phys. 148, 164109 (2018)]. These approaches allow us to extend δt of MD simulations under an isothermal-isobaric condition up to 5 fs with a velocity Verlet integrator. Here, we further improve the isothermal-isobaric MD integration by introducing the group-based evaluations of system temperature and pressure to our previous approach. The group-based scheme increases the accuracy even using inaccurate temperature and pressure evaluations by neglecting the high-frequency vibrational motions of hydrogen atoms. It also improves the overall performance by avoiding iterations in thermostat and barostat updates and by allowing a multiple time step integration such as r-RESPA (reversible reference system propagation algorithm) with our proposed high-precision evaluations of temperature and pressure. Now, the improved integration scheme conserves physical properties of lipid bilayer systems up to δt = 5 fs with velocity Verlet as well as δt = 3.5 fs for fast motions in r-RESPA, respectively.