Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations

作者：Gronbech Jensen Niels^*; Hayre Natha Robert; Farago Oded

来源：Computer Physics Communications, 2014, 185(2): 524-527.

DOI：10.1016/j.cpc.2013.10.006

• Molecular dynamics
• Verlet algorithm
• Simulated Langevin dynamics
• Stochastic differential equations

A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Stormer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.

• 出版日期2014-2