Unwrapping NPT Simulations to Calculate Diffusion Coefficients

JT Bullerjahn and S von Bülow and M Heidari and J Hénin and G Hummer, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 19, 3406-3417 (2023).

DOI: 10.1021/acs.jctc.3c00308

In molecular dynamicssimulations in the NPT ensemble at constantpressure, the size and shape of the periodic simulation box fluctuatewith time. For particle images far from the origin, the rescalingof the box by the barostat results in unbounded position displacements.Special care is thus required when a particle trajectory is unwrappedfrom a projection into the central box under periodic boundary conditionsto a trajectory in full three-dimensional space, e.g., for the calculationof translational diffusion coefficients. Here, we review and comparedifferent schemes in use for trajectory unwrapping. We also specifythe corresponding rewrapping schemes to put an unwrapped trajectoryback into the central box. On this basis, we then identify a schemefor the calculation of diffusion coefficients from NPT simulations,which is a primary application of trajectory unwrapping. In this scheme,the wrapped and unwrapped trajectory are mutually consistent and theirstatistical properties are preserved. We conclude with advice on bestpractice for the consistent unwrapping of constant-pressure simulationtrajectories and the calculation of accurate translational diffusioncoefficients.

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