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

JOURNAL OF COMPUTATIONAL PHYSICS

卷:327

Article

Fernandez-Pendas, Mario¹  Akhmatskaya, Elena^1,2  Sanz-Serna, J. M.³ 

[1] BCAM, Alameda Mazarredo 14, E-48009 Bilbao, Spain

[2] Ikerbasque, Basque Fdn Sci, Maria Diaz de Haro 3, E-48013 Bilbao, Spain

[3] Univ Carlos III Madrid, Dept Matemat, Ave Univ 30, E-28911 Madrid, Spain

关键词: Molecular dynamics;    Hybrid Monte Carlo;    Multi-stage integrators;    Velocity Verlet;    Adaptive integration;    GROMACS;   

DOI  :  10.1016/j.jcp.2016.09.035

来源: Elsevier

【 摘 要 】

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 realizes 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, for the systems where harmonic forces play an important role, the sampling efficiency found in simulations using the AIA is up to 5 times better than the one achieved with other tested schemes. (C) 2016 Elsevier Inc. All rights reserved.

【 授权许可】

Free