Symplectic algorithm for constant-pressure molecular dynamics using a Nosé–Poincaré thermostat

Abstract

We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nosé -Poincaré thermostat, recently developed by Bond, Leimkuhler, and Laird ͓J. Comp. Phys. 151, 114 ͑1999͔͒. This Nosé -Poincaré -Andersen ͑NPA͒ formulation has advantages over the Nosé-Hoover-Andersen approach in that the NPA is Hamiltonian and can take advantage of symplectic integration schemes, which lead to enhanced stability for long-time simulations. The equations of motion are integrated using a generalized leapfrog algorithm ͑GLA͒ and the method is easy to implement, symplectic, explicit, and time reversible. To demonstrate the superior stability of the method we show results for test simulations using a model for aluminum and compare it to a recently developed time-reversible algorithm for Nosé -Hoover-Anderson. In addition, an extension of the NPA to multiple time steps is outlined and a symplectic and time-reversible integration algorithm, based on the GLA, is given.

Does molecular docking reveal alternative chemopreventive mechanism of activation of oxidoreductase by sulforaphane isothiocyanates?

“…Thus, prior to MDs, each activator-1D4A complex was minimized to energy gradient 0,01 kcal mol -1 and then molecular dynamics were performed using forcefields AMBER99 and MMFF94x with the Nosé-Poincaré-Andersen [34,35] algorithm under constant temperature and volume. Although there were several controversies over the application of MMFF94 to MDs [36] we decided to use the MMFF94x variant in our simulations.…”

Entropy and Heat Capacity Calculations by Thermodynamic Approach

“…One of the major advances in molecular dynamics simulations is the discovery that thermostats can be described in a Hamiltonian [6][7][8]. The Nosé-Poincaré thermostat, which is the Hamiltonian version of Nosé-Hoover thermostat, utilizes the Poincaré time transformation H = ν(H − H) where ν is the time scaling factor and H is the value of H regarded as a pure function of time [9].…”

Molecular Simulation in the Canonical Ensemble and Beyond

“…This is termed the Nosé-Poincaré method, and it enables the use of symplectic integration methods. It has been shown to have enhanced stability behavior in simulations [15] compared to Nosé-Hoover based methods when long time interval simulations are performed [5,15,34].…”

“…The numerical method can be constructed by the appropriate composition of numerical integrators solving two subsystems. An explicit generalized Verlet method for the subsystem consisting of q 1 , p 1 can be constructed referring to [34]. Since the velocity Verlet method can be applied to the subsystem consisting of q 2 , p 2 , the overall integrator is explicit.…”