CHARMM-GUI

There are few tools which have democratized molecular mechanics simulations more than CHARMM-GUI. It is an extremely widely-used tool for setting up simulations for a wide variety of systems (biological and materials), including fairly non-trivial systems and enhanced sampling setups. Input scripts including force fields are automatically generated. It is a powerful first step in setting up many simluations, especially for beginners. Take time to play with settings and appreciate some of the (admittedly few) limitations.

Notes and some limitations;

1. Patching missing loops
   • When you want to patch the ends of a missing loop rather than rebuild it:
   • Download the PDB file
   • insert TER lines between missing residues
   • upload this file to CHARMM-GUI
2. MD options may not be up to date, including force fields
3. Configurations still must be equilibrated carefully