Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats

DOI10.1016/J.JCP.2010.09.004MaRDI QIDQ608837zbMATH OpenOpenAlexFDO

Authors R. L. Davidchack

Publication date 26 November 2010

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1412.7067

zbMATH Keywords

backward error analysisconfigurational temperatureDebye relaxation timediffusion coefficientLangevin thermostatNosé-Hoover thermostatnumerical integratorradial distribution functionRichardson extrapolation

Mathematics Subject Classification ID

Stochastic methods (Fokker-Planck, Langevin, etc.) applied to problems in time-dependent statistical mechanics (82C31)

Abstract: We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nos'e-Hoover and Nos'e-Poincar'e) and stochastic (Langevin) thermostats. We propose a couple of simple practical approaches to estimating such errors and taking them into account when computing the averages. We show that it is possible to obtain accurate measurements of various system quantities using step sizes of up to 70% of the stability threshold of the integrator, which for the system of TIP4P liquid water at 300 K corresponds to the step size of about 7 fs.

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Cites work

• Backward Error Analysis for Numerical Integrators
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• scientific article; zbMATH DE number 775665 (Why is no real title available?)
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• Survey of Extrapolation Processes in Numerical Analysis
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• What makes molecular dynamics work?

Cited in

(7)

• On the estimation and correction of discretization error in molecular dynamics averages
• Corrigendum to ``Discretization errors in molecular dynamics simulations with deterministic and stochastic
• A gentle stochastic thermostat for molecular dynamics
• Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
• Molecular dynamics and the accuracy of numerically computed averages
• Comparing the efficiencies of stochastic isothermal molecular dynamics methods
• Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities

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