Input files and scripts for setting up and running MD simulations of PHL7 variants

The repository contains input files and scripts for setting up and running MD simulations of PHL7 variants, along with scripts to analyze the MD data and example output files. The repository directories have the following content: parameters: Forcefield parameter files for protein, solvent, MHET and 4xMHET ligands OPES: Parameters for OPES simulations, free energy profiles HREX_preparation: Input files for HREX simulations HREX_analysis_plumed: PLUMED input files for analyzing enzyme geometric features from HREX simulations MD_analysis_plumed: PLUMED input files for analyzing enzyme geometric features from unbiased MD simulations clustering: Scripts for clustering 4xMHET ligand conformations