Understanding Molecular Dynamics with Stochastic Processes via Real or Virtual Dynamics

Abstract

Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation [J. Chem. Phys. 147, 184104 (2017)] in principle exists in other types of stochastic thermostats as well. The recommended middle scheme [J. Chem. Phys. 147, 034109 (2017)] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation is proposed for understanding efficient stochastic thermostatting processes with molecular dynamics.

arXiv commentarXiv admin note: text overlap with arXiv:1707.04685

References in corpus (6)

• A simple and effective Verlet-type algorithm for simulating Langevin dynamics
• Robust and efficient configurational molecular sampling via Langevin Dynamics
• A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat
• The computation of averages from equilibrium and nonequilibrium Langevin molecular dynamics
• A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics
• Stationary state distribution and efficiency analysis of the Langevin equation via real or virtual dynamics

Cited by in corpus (3)

• On the Numerical Stationary Distribution of Overdamped Langevin Equation in Harmonic System
• Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models
• Geometric Phase Effect in Thermodynamic Properties and in the Imaginary-Time Multi-Electronic-State Path Integral Formulation