Unwrapping NPT Simulations to Calculate Diffusion Coefficients

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.

Automated summary

In molecular dynamics simulations, the size and shape of the simulation box may vary over time. Unbounded position displacements can occur when rescaling the box by the barostat for particle images far from the origin. This necessitates careful trajectory unwrapping and rewrapping methods for accurate calculations of translational diffusion coefficients.