Computationally efficient molecular dynamics integrators with improved sampling accuracy

Abstract

The design of numerical integrators for particle simulations with arbitrary potentials entails fundamental tradeoffs between the accuracy achieved and the amount of computation required. Here we introduce a class of explicit variational integrators designed to achieve high accuracy for quadratic potentials, with little additional computation relative to traditional integrators. We show that, in practice, these new integrators also improve accuracy for classical biomolecular simulations, since the potential in the vicinity of a typical trajectory point in such a simulation is generally well modelled by a quadratic well. In particular, these integrators provide better sampling accuracy for biomolecular simulation than the commonly used Verlet integrators, as indicated by a weaker dependence of simulated ensemble properties on the time step. They also reduce short-timescale energy fluctuations, thus substantially improving the efficiency of Hybrid Monte Carlo methods, and are easy to implement through straightforward modification of codes based on Verlet integrators.

Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans

“…Advancements in massively parallel computing, including new algorithms 42 and hardware, 20 promise sustained progress in carbohydrate modeling. Our findings (e.g., Table 1) are consistent with previous reports, which have concluded that extending carbohydrate simulations to μs timescales is essential to explain experimental observations 43 .…”

Adaptive multi-stage integrators for optimal energy conservation in molecular simulations

“…In order to evaluate the efficiency of the proposed AIA scheme, we compared it in accuracy and performance with the velocity Verlet integrator and with the two-stage integrator (BCSS) of Blanes et al [1]. In addition, some selected tests also involved the two-stage HOH scheme by Predescu et al [27]. All tests probing various integrating schemes have been repeated with three different simulation techniques, MD, HMC and GHMC.…”

“…Section 5 is devoted to numerical results. The performance of the AIA method is compared with the standard velocity Verlet algorithm and the two-stage integrators with the fixed parameter values suggested in [1] and [27]. In all experiments and for each of the criteria employed, the performance of AIA is at least as good as, and often significantly better than, the performances of the Verlet scheme and the fixed parameter two-stage integrators.…”

Editorial

“…On the theoretical and computational side, the special issue entitled 'Quantum Molecular Dynamics', in honour of Prof. William H. Miller (numbers 9, 10 of vol. 110, in 2012) contains a rich variety of articles on all aspects of chemical dynamics, including a perspective by Nobel Laureate Rudolph A. Marcus [11], and articles on defining the hydrogen bond [12], improved integrators for classical molecular dynamics [13], and improvements to ring polymer molecular dynamics for calculating reaction rates [14]. Mixing theory and experiment, the Festschrift for Nobel Laureate Dudley R. Herschbach (numbers 15, 16 of vol.…”