A New Time-Reversible Integrator for Molecular Dynamics Applications

Classical molecular dynamics simulation is performed mostly using the established velocity Verlet integrator or other symplectic propagation schemes. In this work, an alternative formulation of numerical propagators for classical molecular dynamics is introduced based on an expansion of the time evolution operator in series of Chebyshev and Newton polynomials. The suggested propagators have, in principle, arbitrary order of accuracy which can be controlled by the choice of ex...

A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and orientational coordinates are decoded by processing transformations. This allows to overcome the barrier on the order of precision of the integration at a given number of force-torque evaluations per time step. Testing in dynamics of water versus ...

This paper invites the reader to experiment with an easy-to-use MATLAB implementation of Metropolis integrators for Molecular Dynamics (MD) simulation. These integrators are analysis-based, in the sense that they can rigorously simulate dynamics along an infinitely long MD trajectory. Among explicit integrators for MD, they seem to be the only ones that satisfy the fundamental requirement of stability. The schemes can handle stiff or hard-core potentials, and are straightforw...

We address the formulation and analysis of energy and momentum conserving time integration schemes in the context of particle dynamics, and in particular atomic systems. The article identifies three critical aspects of these models that demand a careful analysis when discretized: first, the treatment of periodic boundary conditions; second, the formulation of approximations of systems with three-body interaction forces; third, their extension to atomic systems with functional...

Hamiltonian systems such as the gravitational N-body problem have time-reversal symmetry. However, all numerical N-body integration schemes, including symplectic ones, respect this property only approximately. In this paper, we present the new N-body integrator JANUS, for which we achieve exact time-reversal symmetry by combining integer and floating point arithmetic. JANUS is explicit, formally symplectic and satisfies Liouville's theorem exactly. Its order is even and can b...

Numerical solutions to Newton's equations of motion for chaotic self gravitating systems of more than 2 bodies are often regarded to be irreversible. This is due to the exponential growth of errors introduced by the integration scheme and the numerical round-off in the least significant figure. This secular growth of error is sometimes attributed to the increase in entropy of the system even though Newton's equations of motion are strictly time reversible. We demonstrate that...

An approach is proposed to improve the efficiency of fourth-order algorithms for numerical integration of the equations of motion in molecular dynamics simulations. The approach is based on an extension of the decomposition scheme by introducing extra evolution subpropagators. The extended set of parameters of the integration is then determined by reducing the norm of truncation terms to a minimum. In such a way, we derive new explicit symplectic Forest-Ruth- and Suzuki-like ...

Comment in response to Phys. Rev. Lett. 112, 046401 (2014)

The Stoermer-Verlet-leapfrog group of integrators commonly used in molecular dynamics simulations has long become a textbook subject and seems to have been studied exhaustively. There are, however, a few striking effects in performance of algorithms which are well-known but have not received adequate attention in the literature. A closer view of these unclear observations results in unexpected conclusions. It is shown here that contrary to the conventional point of view, the ...

A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration, whereas orientational positions are expressed in terms of either principal axes or quaternions. As a result, the rigidness of molecules appears to be an integral of motion, despite the atom trajectories are evaluated approximately. The alg...