Unwrapping NPT simulations to calculate diffusion coefficients

Jakob T\'omas BullerjahnS\"oren von B\"ulowMaziar HeidariJ\'er\^ome H\'eninGerhard Hummer

Mar 2023

摘要

In molecular dynamics simulations in the NPT ensemble at constant pressure,the size and shape of the periodic simulation box fluctuate with time. Forparticle images far from the origin, the rescaling of the box by the barostatresults in unbounded position displacements. Special care is thus required whena particle trajectory is unwrapped from a projection into the central box underperiodic boundary conditions to a trajectory in full three-dimensional space,e.g., for the calculation of diffusion coefficients. Here, we review andcompare different schemes in use for trajectory unwrapping. We also specify thecorresponding rewrapping schemes to put an unwrapped trajectory back into thecentral box. On this basis, we then identify a scheme for the calculation ofmeaningful diffusion coefficients, which is a primary application of trajectoryunwrapping. In this scheme, the wrapped and unwrapped trajectory are mutuallyconsistent and their statistical properties are preserved. We conclude withadvice on best practice for the consistent unwrapping of constant-pressuresimulation trajectories and the calculation of accurate translational diffusioncoefficients.

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