A New Time-Reversible Integrator for Molecular Dynamics Applications

Computational efficiency demands discretised, hierarchically organised, and individually adaptive time-step sizes (known as the block-step scheme) for the time integration of N-body models. However, most existing N-body codes adapt individual step sizes in a way that violates time symmetry (and symplecticity), resulting in artificial secular dissipation (and often secular growth of energy errors). Using single-orbit integrations, I investigate various possibilities to reduce ...

We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator splitting techniques similar to those that have been used successfully to generate a variety molecular-dynamics integrators. In numerical experiments, the Impulsive Verlet method is shown to be superior to previous methods with respect to st...

We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order $O(N)$, where $N$ is the number of particles. The algorithm works very effectively when the particles have short range interaction, but it is applicable to each kind of interaction. The code was tested on a Cray ymp el in a simulation of flowing granular material.

An explicit second-order numerical method to integrate the isokinetic equations of motion is derived by fitting circular arcs through every three consecutive points of the discretized trajectory, so that the tangent and the curvature satisfy the equations exactly at every central point. This scheme is reversible and robust, and allows an adaptive step size control. Its performance is tested by computing the thermodynamic properties of simple pair-potential models, and its che...

In molecular simulations, one of the most difficult points is to track the real dynamics of many-body systems from the first principle. The present study shows that step-size dependences have an unexpected effect on simulation results, even when we use the standard high-precision numerical integrators to apply to a simple system with a two-body interaction. The validity of our analysis is checked by the theory of adiabatic approximations.

We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order O(N), where $N$ is the number of particles. The algorithm works very effectively when the particles have short range interaction, but it is applicable to each kind of interaction. The code was tested on a Cray ymp el in a simulation of flowing granular material.

A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the time step, all the conservation laws inherent in the description without breaking the time reversibility. As a result, an implicit second-order algorithm is derived and applied to pure as well as spin liquids for which the dynamics is chara...

A new algorithm is introduced to integrate the equations of rotational motion. The algorithm is derived within a leapfrog framework and the quantities involved into the integration are mid-step angular momenta and on-step orientational positions. Contrary to the standard implicit method by Fincham [Mol. Simul., 8, 165 (1992)], the revised angular momentum approach presented corresponds completely to the leapfrog idea on interpolation of dynamical variables without using any e...

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. Th...

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems, however, create the need for approximations to the standard MD methods and for uncertainty quantification and reliability assessment of those approximations. In this paper, we exploit the intrinsic two-scale nature of MD to construct a clas...