Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them.
Licenses for this software are available, for a fee, to people and groups working in academia.
The CHARMM force fields for proteins include: united-atom (sometimes termed extended atom) CHARMM19,[6] all-atom CHARMM22[7] and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF.
[8] In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water.
In 2006, a special version of CHARMM22/CMAP was reparametrized for consistent use with implicit solvent GBSW.
The bond, angle, dihedral, and nonbonded terms are similar to those found in other force fields such as AMBER.
The CHARMM force field also includes an improper term accounting for out-of-plane bending (which applies to any set of four atoms that are not successively bonded), where
Some force fields may be combined, for example CHARMM22 and CHARMM27 for the simulation of protein-DNA binding.
Likewise, these force fields may be used within other molecular dynamics programs that support them.
In 2009, a general force field for drug-like molecules (CGenFF) was introduced.
It "covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds".
[12] The general force field is designed to cover any combination of chemical groups.
Users are repeatedly warned in Mackerell's website not to use the CGenFF parameters for molecules for which specialized force fields already exist (as mentioned above for proteins, nucleic acids, etc.).
CHARMM also includes polarizable force fields using two approaches.
[15][16] Parameters for all of these force fields may be downloaded from the Mackerell website for free.
[17] The CHARMM program allows for generating and analysing a wide range of molecular simulations.
The most basic kinds of simulation are minimizing a given structure and production runs of a molecular dynamics trajectory.
More advanced features include free energy perturbation (FEP), quasi-harmonic entropy estimation, correlation analysis and combined quantum, and quantum mechanics–molecular mechanics (QM/MM) methods.
This is an inevitable result of the many outlooks and groups working on CHARMM worldwide.
The changelog file, and CHARMM's source code, are good places to look for the names and affiliations of the main developers.
The involvement and coordination by Charles L. Brooks III's group at the University of Michigan is salient.
Around 1969, there was considerable interest in developing potential energy functions for small molecules.
Karplus and his then graduate student Bruce Gelin decided the time was ripe to develop a program that would make it possible to take a given amino acid sequence and a set of coordinates (e.g., from the X-ray structure) and to use this information to calculate the energy of the system as a function of the atomic positions.
Karplus has acknowledged the importance of major inputs in the development of the (at the time nameless) program, including: In the 1980s, finally a paper appeared and CHARMM made its public début.
For the publication, Bob Bruccoleri came up with the name HARMM (HARvard Macromolecular Mechanics), but it seemed inappropriate.
Karplus said: "I sometimes wonder if Bruccoleri's original suggestion would have served as a useful warning to inexperienced scientists working with the program.
"[18] CHARMM has continued to grow and the latest release of the executable program was made in 2015 as CHARMM40b2.
The general syntax for using the program is: charmm -i filename.inp -o filename.out Docking@Home, hosted by University of Delaware, one of the projects which use an open-source platform for the distributed computing, BOINC, used CHARMM to analyze the atomic details of protein-ligand interactions in terms of molecular dynamics (MD) simulations and minimizations.