Abstract
Molecular dynamics is a simulation technique used to predict the physical properties of systems based on their chemical structure and evolution of their atomic constituents. For these predictions to be reliable, it is critical that the simulation has reached convergence, whereby representative sampling of the phase space has been gathered. We show that the commonly used root mean square deviation is an unsuitable convergence descriptor for systems featuring surfaces and interfaces. We then present an effective criterion, embodied in the analysis tool DynDen, based on convergence of the linear partial density of all components in the simulation. With a variety of examples we demonstrate the usage of DynDen for the assessment of convergence, as well as for identification of slow dynamical processes, which can be easily missed with conventional analysis. Program summaryProgram title: DynDenCPC Library link to program files:https://doi.org/10.17632/dfb34rpyw2.1Developer's repository link:https://github.com/punkpony/DynDenLicensing provisions: GNU General Public License 3Programming Language: Python 3.XExternal Routines/Libraries: MDAnalysis, numpy, matplotlibNature of problem: assessment of convergence in molecular dynamics simulations of interfacesSolution method: reporting on the convergence of correlation of the linear density profiles of each individual system component
Highlights
Molecular dynamics (MD) is a computational technique aimed at inferring the physical and chemical properties of a molecular system by investigating its atomic structure and associated dynamics
Using simulation data from our previous work on interfaces [6,7,8], we show that root mean square deviation (RMSD) is insufficient to determine whether the simulation is biased by undersampling, leading to erroneous interpretations
An RMSD analysis indicates that the smaller system reaches convergence within 5 ns, while the larger system is still evolving after 40 ns
Summary
Molecular dynamics (MD) is a computational technique aimed at inferring the physical and chemical properties of a molecular system by investigating its atomic structure and associated dynamics. Organic components in an oil reservoir are constantly undergoing slow evolution on geological timescales In such case, both experiments and models probe the current state of the reservoir. RMSD is a global system property and, while simulations of interfaces often incorporate bulk, researchers are usually interested in assessing the local interactions of nearinterface regions, at a defect or a specific surface site. In these regions, dynamics are different from those in the bulk, as they are restricted and, slower. When the linear density of each component in the system no longer evolves, one may assume the system to be kinetically converged
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