Simple quantitative tests to validate sampling from thermodynamic ensembles

Abstract

It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow sensitive determination of whether a de- sired thermodynamic ensemble is properly sampled. We demonstrate the utility of these tests for model systems and for molecular dynamics simulations in a range of situations, includ- ing constant volume and constant pressure simulations, and describe an implementation of the tests designed for end users.

48 pages, 4 figures

References in corpus (3)

• Canonical sampling through velocity-rescaling
• Statistically optimal analysis of samples from multiple equilibrium states
• Non-ergodicity of Nose-Hoover dynamics

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• Refinement of Thermostated Molecular Dynamics Using Backward Error Analysis