Data for Depletion forces from interacting crowders

The data archived here includes all results from the post-processing analysis of molecular dynamics simulations, cluster analysis, and free energy calculations referenced in the attached paper titled "Depletion forces from interacting crowders." This dataset offers a reusable computational framework and data resource for exploring the depletion force between two colloids immersed in a medium of either repulsively or attractively interacting crowder particles. We have conducted enhanced sampling molecular dynamics simulations using the open-source software LAMMPS, the ‘colvars’ package to implement umbrella sampling within LAMMPS, and an open-source package developed by the Grossfield Lab (http://membrane.urmc.rochester.edu/content/wham/) to perform WHAM calculations . This archive contains subfolders for each figure, either individually, or grouped for convenience and similarity. Within each figure subfolder, the user can find a folder titled “analysis_and_plotting” which contains the post processing scripts and results and plots generated from them, and a folder titled “simulation_and_input_files” which provides examples of preparing and obtaining the raw data.