The adaptive Verlet method

This is the published version, also available here: http://dx.doi.org/10.1137/S1064827595284658.We discuss the integration of autonomous Hamiltonian systems via dynamical rescaling of the vector field (reparameterization of time). Appropriate rescalings (e.g., based on normalization of the vector field or on minimum particle separation in an N-body problem) do not alter the time-reversal symmetry of the flow, and it is desirable to maintain this symmetry under discretization. For standard form mechanical systems without rescaling, this can be achieved by using the explicit leapfrog--Verlet method; we show that explicit time-reversible integration of the reparameterized equations is also possible if the parameterization depends on positions or velocities only. For general rescalings, a scalar nonlinear equation must be solved at each step, but only one force evaluation is needed. The new method also conserves the angular momentum for an N-body problem. The use of reversible schemes, together with a step control based on normalization of the vector field (arclength reparameterization), is demonstrated in several numerical experiments, including a double pendulum, the Kepler problem, and a three-body problem

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

We introduce a new Adaptive Integration Approach (AIA) to be used in a wide range of molecular simulations. Given a simulation problem and a step size, the method automatically chooses the optimal scheme out of an available family of numerical integrators. Although we focus on two-stage splitting integrators, the idea may be used with more general families. In each instance, the system-specific integrating scheme identified by our approach is optimal in the sense that it provides the best conservation of energy for harmonic forces. The AIA method has been implemented in the BCAM-modified GROMACS software package. Numerical tests in molecular dynamics and hybrid Monte Carlo simulations of constrained and unconstrained physical systems show that the method successfully realises the fail-safe strategy. In all experiments, and for each of the criteria employed, the AIA is at least as good as, and often significantly outperforms the standard Verlet scheme, as well as fixed parameter, optimized two-stage integrators. In particular, the sampling efficiency found in simulations using the AIA is up to 5 times better than the one achieved with other tested schemes

Accurate and efficient splitting methods for dissipative particle dynamics

We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales. We propose a new splitting method that is able to substantially improve the accuracy and efficiency of DPD simulations in a wide range of the friction coefficients, particularly in the extremely large friction limit that corresponds to a fluid-like Schmidt number, a key issue in DPD. Various numerical experiments on both equilibrium and transport properties are performed to demonstrate the superiority of the newly proposed method over popular alternative schemes in the literature

Pathwise Accuracy and Ergodicity of Metropolized Integrators for SDEs

Metropolized integrators for ergodic stochastic differential equations (SDE) are proposed which (i) are ergodic with respect to the (known) equilibrium distribution of the SDE and (ii) approximate pathwise the solutions of the SDE on finite time intervals. Both these properties are demonstrated in the paper and precise strong error estimates are obtained. It is also shown that the Metropolized integrator retains these properties even in situations where the drift in the SDE is nonglobally Lipschitz, and vanilla explicit integrators for SDEs typically become unstable and fail to be ergodic.Comment: 46 pages, 5 figure

From Classical to Quantum and Back: Hamiltonian Adaptive Resolution Path Integral, Ring Polymer, and Centroid Molecular Dynamics

Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, such as ring polymer and centroid molecular dynamics, which allow the approximate calculation of both quantum statistical and quantum dynamical properties. To this end, we derive a new integration algorithm which also makes use of multiple time-stepping. The scheme is validated via adaptive classical--path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins

Using Bayes formula to estimate rates of rare events in transition path sampling simulations

Transition path sampling is a method for estimating the rates of rare events in molecular systems based on the gradual transformation of a path distribution containing a small fraction of reactive trajectories into a biased distribution in which these rare trajectories have become frequent. Then, a multistate reweighting scheme is implemented to postprocess data collected from the staged simulations. Herein, we show how Bayes formula allows to directly construct a biased sample containing an enhanced fraction of reactive trajectories and to concomitantly estimate the transition rate from this sample. The approach can remediate the convergence issues encountered in free energy perturbation or umbrella sampling simulations when the transformed distribution insufficiently overlaps with the reference distribution.Comment: 11 pages, 8 figure