Editing CHARMM (section)

== Force fields ==
The CHARMM [[force field (chemistry)|force field]]s for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19,<ref name=Reiher1985>{{cite thesis |author=Reiher, III WH |title=Theoretical studies of hydrogen bonding |publisher=Harvard University| year=1985}}</ref> all-atom CHARMM22<ref name=MacKerell1998>{{cite journal |author=MacKerell AD Jr| year=1998 |title=All-atom empirical potential for molecular modeling and dynamics studies of proteins |journal=J Phys Chem B |volume=102 |issue=18 |pages=3586–3616 |doi=10.1021/jp973084f|display-authors=etal |pmid=24889800}}</ref> and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF.<ref name=MacKerell2004a>{{cite journal |vauthors=MacKerell AD Jr, Feig M, Brooks III CL |year=2004 |title=Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations |journal=J Comput Chem |volume=25 |pages=1400–1415 |doi=10.1002/jcc.20065 |pmid=15185334 |issue=11|s2cid=11076418 }}</ref> In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermore, CHARMM22 is parametrized for the TIP3P explicit [[water model]]. Nevertheless, it is often used with [[implicit solvent]]s. In 2006, a special version of CHARMM22/CMAP was reparametrized for consistent use with implicit solvent GBSW.<ref name=Brooks2006>{{cite journal |vauthors=Brooks CL, Chen J, Im W |year=2006 |title=Balancing solvation and intramolecular interactions: toward a consistent generalized born force field (CMAP opt. for GBSW) |journal=J Am Chem Soc |volume=128 |pages=3728–3736 |doi=10.1021/ja057216r |pmid=16536547 |issue=11 |pmc=2596729}}</ref>

The CHARMM22 force field has the following potential energy function:<ref name=MacKerell1998 /><ref>{{Cite journal |last1=Vanommeslaeghe |first1=K. |last2=MacKerell |first2=A. D. |date=May 2015 |title=CHARMM additive and polarizable force fields for biophysics and computer-aided drug design |journal=Biochimica et Biophysica Acta (BBA) - General Subjects |volume=1850 |issue=5 |pages=861–871 |doi=10.1016/j.bbagen.2014.08.004 |issn=0006-3002 |pmc=4334745 |pmid=25149274}}</ref>

<math>\begin{align}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{align}</math>

The bond, angle, dihedral, and nonbonded terms are similar to those found in other force fields such as [[AMBER#Functional_form|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 <math>k_\omega</math> is the force constant and <math>\omega-\omega_0</math> 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; <math>k_u</math> is the force constant and <math>u</math> is the distance between the 1,3 atoms.

For [[DNA]], [[RNA]], and [[lipid]]s, CHARMM27<ref name=MacKerell2001>{{cite journal |vauthors=MacKerell AD Jr, Banavali N, Foloppe N |year=2001 |title=Development and current status of the CHARMM force field for nucleic acids |journal=Biopolymers |volume=56 |pages=257–265 |doi=10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W |pmid=11754339 |issue=4|s2cid=19502363 }}</ref> 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".<ref name=Vanommeslaeghe>{{cite journal |vauthors=Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, ((Mackerell AD Jr)) |year=2009 |title=CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields |journal=J Comput Chem |volume= 31| pages= 671–90| doi=10.1002/jcc.21367 |pmc=2888302 |pmid=19575467 |issue=4}}</ref> 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).<ref name=Patel2004a>{{cite journal |vauthors=Patel S, Brooks CL 3rd |year=2004 |title=CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations |journal=J Comput Chem |volume=25 |pages=1–15 |doi=10.1002/jcc.10355 |pmid=14634989 |issue=1|s2cid=39320318 }}</ref><ref name=Patel2004b>{{cite journal |vauthors=Patel S, Mackerell AD Jr, Brooks CL 3rd |year=2004 |title=CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model |journal=J Comput Chem |volume=25 |pages=1504–1514 |doi=10.1002/jcc.20077 |pmid=15224394 |issue=12|s2cid=16741310 |doi-access=free }}</ref> The other is based on the [[Drude particle|Drude]] shell or dispersion oscillator model.<ref name="Lamoureux">{{cite journal |vauthors=Lamoureux G, Roux B |year=2003 |title=Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm |journal=J Chem Phys |volume=119 |issue=6 |pages=3025–3039 |doi=10.1063/1.1589749|bibcode= 2003JChPh.119.3025L|doi-access=free }}</ref><ref name="Lamoureux3">{{cite journal |vauthors=Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD |year=2006 |title=A polarizable model of water for molecular dynamics simulations of biomolecules |journal=Chem Phys Lett |volume=418 |issue=1–3 |pages=245–249 |doi=10.1016/j.cplett.2005.10.135|bibcode= 2006CPL...418..245L}}</ref>

Parameters for all of these force fields may be downloaded from the Mackerell website for free.<ref>[http://mackerell.umaryland.edu/CHARMM_ff_params.html Mackerell website]</ref>