TY - JOUR

T1 - Unwrapping NPT Simulations to Calculate Diffusion Coefficients

AU - Bullerjahn, Jakob Tómas

AU - Von Bülow, Sören

AU - Heidari, Maziar

AU - Hénin, Jérôme

AU - Hummer, Gerhard

PY - 2023

Y1 - 2023

N2 - 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 coefficients from NPT simulations, which is a primary application of trajectory unwrapping. In this scheme, the wrapped and unwrapped trajectory are mutually consistent and their statistical properties are preserved. We conclude with advice on best practice for the consistent unwrapping of constant-pressure simulation trajectories and the calculation of accurate translational diffusion coefficients.

AB - 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 coefficients from NPT simulations, which is a primary application of trajectory unwrapping. In this scheme, the wrapped and unwrapped trajectory are mutually consistent and their statistical properties are preserved. We conclude with advice on best practice for the consistent unwrapping of constant-pressure simulation trajectories and the calculation of accurate translational diffusion coefficients.

U2 - 10.1021/acs.jctc.3c00308

DO - 10.1021/acs.jctc.3c00308

M3 - Journal article

C2 - 37257090

VL - 19

SP - 3406

EP - 3417

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 11

ER -