Computing Transport Coefficients from Molecular Dynamics using Mean-Squared Displacements

This code uses output files from LAMMPS molecular dynamics simulations to compute Onsager transport coefficients in electrolyte solutions. The transport coefficients are computed using Einstein relations, which give the transport coefficients based on the positions or mean-square displacements. The Jupyter notebook contains the equations used for the calculation as well as instructions for preparing the input files from LAMMPS simulations. We provide example simulation data (in the example-data folder), as well as the output that should be generated from running the example code. The example simulation data is from coarse-grained simulations of polyelectrolyte solutions (see https://doi.org/10.1021/acs.macromol.0c02001).