CHARMM

CHARMM

Accelrys
Initial release	1983; 41 years ago (1983)
Stable release	c47b1 / 2022; 2 years ago (2022)[1]
Preview release	c48a1 / 2022; 2 years ago (2022)[1]
Written in	ARM, Nvidia GPU; Cray XT4, XT5[2]
Available in	English
Type	Molecular dynamics
License	Proprietary
Website	www.academiccharmm.org

Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of

to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.

Force fields

The CHARMM

The CHARMM22 force field has the following potential energy function:[7]^[10]

${\displaystyle {\begin{aligned}V=&\sum _{bonds}k_{b}(b-b_{0})^{2}+\sum _{angles}k_{\theta }(\theta -\theta _{0})^{2}+\sum _{dihedrals}k_{\phi }[1+cos(n\phi -\delta )]\\&+\sum _{impropers}k_{\omega }(\omega -\omega _{0})^{2}+\sum _{Urey-Bradley}k_{u}(u-u_{0})^{2}\\&+\sum _{nonbonded}\left(\epsilon _{ij}\left[\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{12}-2\left({\frac {R_{min_{ij}}}{r_{ij}}}\right)^{6}\right]+{\frac {q_{i}q_{j}}{\epsilon _{r}r_{ij}}}\right)\end{aligned}}}$

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 ${\displaystyle k_{\omega }}$ is the force constant and ${\displaystyle \omega -\omega _{0}}$ is the out-of-plane angle. The Urey-Bradley term is a cross-term that accounts for 1,3 nonbonded interactions not accounted for by the bond and angle terms; ${\displaystyle k_{u}}$ is the force constant and ${\displaystyle u}$ is the distance between the 1,3 atoms.

For DNA, RNA, and lipids, CHARMM27^[11] is used. Some force fields may be combined, for example CHARMM22 and CHARMM27 for the simulation of protein-DNA binding. Also, parameters for NAD+, sugars, fluorinated compounds, etc., may be downloaded. These force field version numbers refer to the CHARMM version where they first appeared, but may of course be used with subsequent versions of the CHARMM executable program. 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. This inevitably comes with a decrease in accuracy for representing any particular subclass of molecules. 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. One is based on the fluctuating charge (FQ) model, also termed Charge Equilibration (CHEQ).^[13][14] The other is based on the Drude shell or dispersion oscillator model.^[15][16]

Parameters for all of these force fields may be downloaded from the Mackerell website for free.^[17]

Molecular dynamics program

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

) methods.

CHARMM is one of the oldest programs for molecular dynamics. It has accumulated many features, some of which are duplicated under several keywords with slight variants. 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.

Software history

Around 1969, there was considerable interest in developing potential energy functions for small molecules. CHARMM originated at Martin Karplus's group at Harvard. 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:

• Schneior Lifson's group at the Weizmann Institute, especially from Arieh Warshel who went to Harvard and brought his consistent force field (CFF) program with him
• Harold Scheraga's group at Cornell University
• Awareness of Michael Levitt's pioneering energy calculations for proteins

In the 1980s, finally a paper appeared and CHARMM made its public début. Gelin's program had by then been considerably restructured. For the publication, Bob Bruccoleri came up with the name HARMM (HARvard Macromolecular Mechanics), but it seemed inappropriate. So they added a C for Chemistry. 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.

Running CHARMM under Unix-Linux

The general syntax for using the program is:

charmm -i filename.inp -o filename.out

• charmm – The name of the program (or script which runs the program) on the computer system being used.
• filename.inp – A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and force field (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files). One can then modify the molecules (adding hydrogens, changing secondary structure). The calculation section can include energy minimization, dynamics production, and analysis tools such as motion and energy correlations.
• filename.out – The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications. The values for temperature, energy pressure, etc. are output at that frequency.

Volunteer computing

(MD) simulations and minimizations.

World Community Grid, sponsored by IBM, ran a project named The Clean Energy Project^[19] which also used CHARMM in its first phase which has completed.

See also

References

External links

• Official website, with documentation and helpful discussion forums
• Official website, BIOVIA
• CHARMM tutorial Archived 2010-10-05 at the Wayback Machine
• MacKerell website, hosts package of force field parameters for CHARMM
• C.Brooks website
• CHARMM page at Harvard
• Roux website Archived 2006-10-12 at the Wayback Machine
• Bernard R. Brooks Group website
• Docking@Home
• CHARMM-GUI project
• CHARMMing (CHARMM Interface and Graphics) Archived 2008-08-20 at the Wayback Machine
• CHARMM Tutorial