Pharmacon: A Molecular Dynamics Simulation Analysis Toolkit

Abstract

We present the Pharmacon toolkit, a pure Python command-line software package for analyzing molecular dynamics (MD) simulations of biomacromolecules. Pharmacon supports trajectories generated by widely used MD simulation engines, such as Amber, Gromacs, CHARMM, NAMD, and OpenMM. Pharmacon is written entirely in Python and uses popular third-party libraries, including MDAnalysis for trajectory handling and NumPy for data processing. The toolkit provides a streamlined, automated workflow that simplifies the routine analysis and postprocessing of MD simulation results of biomacromolecular complexes, making them more accessible and reproducible by aggregating many tedious and time-consuming tasks into a single command-line workflow. As a proof of concept, we applied Pharmacon to analyze, in comparison with other toolkits, results from MD simulations, including intermolecular interactions and geometric measures, across different test protein complexes, including three membrane proteins and one soluble protein complex.