The present repository serves to maintain a copy of the used scripts in my thesis. "Computational optimization of bioadsorvents for the removal of pharmaceuticals from water". Their usage is free and encouraged, but beware: I had zero to no experience creating them. With this being said, they are probably very archaiac and non-optimized. Use at your own risk. >> amc.py Multi Conformational Analysis tool, as described in Section 2, performs an heating/quenching cycle in order to gather the [int] conformations with lowest energies. Uses GROMACS software. >> martin.py Draws activated carbon residue from scratch, using input data from experiemental essays >> flora.py Clusters residues from library to create carbon model, then runs minimization. Adds pharmaceuticals and performs molecular mechanics simulations, using GROMACS software. >>gcmc.py Uses RASPA 2.0 software to perform Monte Carlo simulations in the Grand Canonical Ensemble. inputAds.dat file can be used to perform batch simulations with different concentrations. >>recover.py Searches directories for RASPA 2.0 output files and gathers them in a human-friendly output. >>toolBox.py Data and functions used by several other scripts. The present scripts may not be up to date. The working directory architecture may require the presence of certain folders and files such as the forcefield for GROMACS. Any questions or requests can be directed to jose.manuel.pereira@ua.pt Thank you, José Pereira