This is a collection of scripts to calculate small-molecule permeability through gram-negative outer membrane porins. These scripts were originally written by Ricardo Ferreira and accompany the following publications:
Simulation-guided engineering of antibiotics for improved bacterial uptake, Ricardo Ferreira, Valeria Aguilar, Ana Villamil Giraldo, and Peter Kasson, doi:10.1101/2020.10.08.330332. Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics, Ricardo Ferreira and Peter Kasson, doi:10.1021/acsinfecdis.9b00201.
At current time, the scripts should not be considered production-quality software but rather illustrative of the approach. Some manual adjustment may be required to obtain correct umbrella windows for a given simulation, for example. Please check results carefully.