Group-based evaluation of temperature and pressure for molecular dynamics simulation with a large time step
Jaewoon Jung, Yuji Sugita
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.