Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations

DOI10.1016/J.CPC.2013.10.006MaRDI QIDQ339756zbMATHOpenAlexFDO

Authors Niels Grønbech-Jensen, Natha Robert Hayre, Oded Farago

Publication date 11 November 2016

Published in Computer Physics Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1303.7011

zbMATH Keywords

stochastic differential equationsmolecular dynamicssimulated Langevin dynamicsVerlet algorithm

Mathematics Subject Classification ID

Stochastic ordinary differential equations (aspects of stochastic analysis) (60H10) Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31)

Abstract: A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps, is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as an example that can be easily simulated by all three packages. Contrary to existing methods, the new thermostat exhibits no detectable changes in the sampling statistics as the time step is varied in the entire numerical stability range. The simple form of the method, which we express in the three common forms (Velocity-Explicit, Stormer-Verlet, and Leap-Frog), allows for easy implementation within existing molecular simulation packages to achieve faster and more accurate results with no cost in either computing time or programming complexity.

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Cites work

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Cited in

(7)

• Algorithms for Brownian dynamics across discontinuities
• Langevin thermostat for robust configurational and kinetic sampling
• Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats
• The effects of intrinsic dynamical ghost modes in discrete-time Langevin simulations
• Application of underdamped Langevin dynamics simulations for the study of diffusion from a drug-eluting stent
• A beginner's short guide to membrane biophysics
• Thermostats for ``slow configurational modes

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