A New Time-Reversible Integrator for Molecular Dynamics Applications

A consequent approach is proposed to construct symplectic force-gradient algorithms of arbitrarily high orders in the time step for precise integration of motion in classical and quantum mechanics simulations. Within this approach the basic algorithms are first derived up to the eighth order by direct decompositions of exponential propagators and further collected using an advanced composition scheme to obtain the algorithms of higher orders. Contrary to the scheme by Chin an...

Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular dynamics. These methods capture the crosstalk between atomic and coarse-grained scales arising in macromolecular systems. This crosstalk is accounted for by Trotter factorization, which is used to separate the all-atom from the coarse-grained phas...

The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they lack any relationship with real-life experiments, as most of these tests are performed in a constant temperature environment that allows energy exchanges. So, within the framework of molecular dynamics, the Newtonian evolution equations need t...

Time-symmetric integration schemes share with symplectic schemes the property that their energy errors show a much better behavior than is the case for generic integration schemes. Allowing adaptive time steps typically leads to a loss of symplecticity. In contrast, time symmetry can be easily maintained, at least for a continuous choice of time step size. In large-scale N-body simulations, however, one often uses block time steps, where all time steps are forced to take on v...

In this work we introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble. In particular, we consider the equations arising from the so-called density dynamics algorithm with any possible type of thermostat and provide an integrator that preserves the invariant distribution. Our integrator thus constitutes a unified framework that allows the study and comparison of different thermostats and of their influence on the equi...

We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting via the Lennard-Jones pairwise potential, was also written in Python programming language in both top-down and function-based designs.

A new symplectic time-reversible algorithm for numerical integration of the equations of motion in magnetic liquids is proposed. It is tested and applied to molecular dynamics simulations of a Heisenberg spin fluid. We show that the algorithm exactly conserves spin lengths and can be used with much larger time steps than those inherent in standard predictor-corrector schemes. The results obtained for time correlation functions demonstrate the evident dynamic interplay between...

We present a simple algorithm to switch between $N$-body time integrators in a reversible way. We apply it to planetary systems undergoing arbitrarily close encounters and highly eccentric orbits, but the potential applications are broader. Upgrading an ordinary non-reversible switching integrator to a reversible one is straightforward and introduces no appreciable computational burden in our tests. Our method checks if the integrator during the time step violates a time-symm...

In the formalism of constrained mechanics, such as that which underlies the SHAKE and RATTLE methods of molecular dynamics, we present an algorithm to convert any one-step integration method to a variational integrator of the same order. The one-step method is arbitrary, and the conversion can be automated, resulting in a powerful and flexible approach to the generation of novel variational integrators with arbitrary order.

We present a practical numerical method for evaluating the Lagrange multipliers necessary for maintaining a constrained linear geometry of particles in dynamical simulations. The method involves no iterations, and is limited in accuracy only by the numerical methods for solving small systems of linear equations. As a result of the non-iterative and exact (within numerical accuracy) nature of the procedure there is no drift in the constrained geometry, and the method is theref...