Supporting Files for PyCPET - Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics

Here are supporting files for the paper "PyCPET - Computing Heterogeneous 3D Protein Electric Fields and Their Dynamics"

There are three tar files, for each system demonstrated in this study. The folder structures are nearly identical among them; they each contain:

Benchmarks for radius and sample/step size convergence (PyCPET)

Parameters for molecular dynamics simulations (in the form of AMBER prmtop files)

Production run simulation files, at the sampling level of the field topology (once every 0.1ns)

Clustering results, with representative field frames (PyCPET)

For all PyCPET functions above, options.json files are given as examples of how to run cpet.py. Please stay up-to-date on any changes at https://github.com/pujanajmera/pycpet/tree/main to ensure the script is running correctly

Additionally, the Alcohol Dehydrogenase folder contains PCA results.