Welcome to the CpHMD-container wiki!

Here you will be able to find all information and details regarding the CpHMD workflow used by the MMS lab lead by Miguel Machuqueiro in Lisbon! We will try to provide both details on how CpHMD works and tutorials on how you can perform simulations of your proteins with the CpHMD methodology!

As of now, CpHMD has been containerized for global usage and within the container we provide:

• GROMACS 2024.3 binaries: The main program where the MD part of CpHMD is done
• Delphi v5.1 : Program for Poisson-Boltzmann calculations, provided by ((Insert the group and rights for delphi))
• petit: Program used for the Monte Carlo calculation done
• Force-Fields: We provide 3 force-fields within the container GROMOS 54a7, CHARMM36m, and AMBER16sb with the necessary titratable residues and their tautomers.
• Sts: Databases for the tautomers required for the exchanges in tautomers for PB/MC cycles.
• Databases: Delphi charge and radii databases for PB calculations

• CpHMD workflow
• CpHMD settings documentation
• Supported residues per Force Field
• How to add a new molecule to CpHMD
• How to parameterize a new titratable molecule

• CpHMD: Protein in Solution
• CpHMD: Protein+Membrane system
• CpHMD: Protein+Solute as include
• CpHMD: Protein+Solute in the FF