Molecular modeling and simulations provide detailed atomic-level descriptions and understanding of the mechanisms and dynamics for chemical processes. Often, one requires the model system to be in equilibrium so that certain thermodynamic properties can be accurately calculated. However, it is not trivial to determine if a system has been properly equilibrated, and many studies only carry out simple and qualitative assessments such as visual inspections of the simulated trajectories and/or the plotted time series of thermodynamic variables (e.g. energy and temperature). Algorithms for quantitative assessments have been published, but their application has been hindered by the lack of user-friendly computer programs that are freely available. Here we developed a user-friendly open-source Perl script, EquCheck, where we have implemented four quantitative assessments to help determine equilibrium. The assessments are based on rigorous statistical analyses of the time series of a thermodynamic variable provided by the user.

Quantitative assessments of model equilibration in molecular dynamics simulations

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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