CHARMM

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program capable of running all or united atom energy minimization, Molecular Dynamics and Monte Carlo simulations. We don't often use CHARMM on its own, but rather use it through the interface to OPTIM and GMIN. There are however a few occasions when you can use CHARMM itself to calculate useful properties i.e. energy, radius of gyration, rmsd from a reference structure, or you might want to convert between .crd and .pdb formats. CHARMM can do all these things for you if you give it the correct input. Below are detailed a few of the most useful features of CHARMM. If you want to find out more about what else you can do, search the documentation, preferably on one of the clusters in the doc directory or online here. This is for a more recent version of the code but you should be able to find what you need.

Tutorials

• input file basics - the bare minimum you need to include!
• Generating pdb, crd and psf for a peptide sequence
• converting between '.crd' and '.pdb'
• Calculating energy of a conformation
• loops and variables in CHARMM
• using CHARMM to orient molecules at the origin
• atom selection in CHARMM - including the .around. syntax for spatial selection
• calculating order parameters - useful for classifying biological systems