Refinement of thermostated molecular dynamics using backward error analysis.

Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical integration may lead to deviations from equipartition. Fortunately, backward error analysis allows us to obtain a higher-order estimate of the quantity that is actually subject to equipartition.

Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water.

Sets of atoms collectively behaving as rigid bodies are often used in molecular dynamics to model entire molecules or parts thereof. This is a coarse-graining strategy that eliminates degrees of freedom and supposedly admits larger time steps without abandoning the atomistic character of a model. In this paper, we rely on a particular factorization of the rotation matrix to simplify the mechanical formulation of systems containing rigid bodies.