Unwrapping NPT Simulations to Calculate Diffusion Coefficients.

ABSTRACT: In molecular dynamics simulations in the NPT ensemble at constant pressure, the size and shape of the periodic simulation box fluctuate with time. For particle images far from the origin, the rescaling of the box by the barostat results in unbounded position displacements. Special care is thus required when a particle trajectory is unwrapped from a projection into the central box under periodic boundary conditions to a trajectory in full three-dimensional space, e.g., for the calculation of translational diffusion coefficients. Here, we review and compare different schemes in use for trajectory unwrapping. We also specify the corresponding rewrapping schemes to put an unwrapped trajectory back into the central box. On this basis, we then identify a scheme for the calculation of diffusion c

SUBMITTER: Bullerjahn JT 

PROVIDER: S-EPMC10269326 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature