Editing Molecular dynamics (section)

=== Polarizable potentials ===

{{Main|Force field (chemistry)|l1=Force field}}
Most classical force fields implicitly include the effect of [[polarizability]], e.g., by scaling up the partial charges obtained from quantum chemical calculations. These partial charges are stationary with respect to the mass of the atom. But molecular dynamics simulations can explicitly model polarizability with the introduction of induced dipoles through different methods, such as [[Drude particle]]s or fluctuating charges. This allows for a dynamic redistribution of charge between atoms which responds to the local chemical environment.

For many years, polarizable MD simulations have been touted as the next generation. For homogenous liquids such as water, increased accuracy has been achieved through the inclusion of polarizability.<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 |pages=245–249 |doi=10.1016/j.cplett.2005.10.135|bibcode= 2006CPL...418..245L }}</ref><ref name="Sokhan2015">{{cite journal | vauthors = Sokhan VP, Jones AP, Cipcigan FS, Crain J, Martyna GJ | title = Signature properties of water: Their molecular electronic origins | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 20 | pages = 6341–6346 | date = May 2015 | pmid = 25941394 | pmc = 4443379 | doi = 10.1073/pnas.1418982112 | doi-access = free | bibcode = 2015PNAS..112.6341S }}</ref><ref name="Cipcigan">{{cite journal | vauthors = Cipcigan FS, Sokhan VP, Jones AP, Crain J, Martyna GJ | title = Hydrogen bonding and molecular orientation at the liquid-vapour interface of water | journal = Physical Chemistry Chemical Physics | volume = 17 | issue = 14 | pages = 8660–8669 | date = April 2015 | pmid = 25715668 | doi = 10.1039/C4CP05506C | doi-access = free | bibcode = 2015PCCP...17.8660C | hdl = 20.500.11820/0bd0cd1a-94f1-4053-809c-9fb68bbec1c9 | hdl-access = free }}</ref> Some promising results have also been achieved for proteins.<ref>{{cite journal | vauthors = Mahmoudi M, Lynch I, Ejtehadi MR, Monopoli MP, Bombelli FB, Laurent S | title = Protein-nanoparticle interactions: opportunities and challenges | journal = Chemical Reviews | volume = 111 | issue = 9 | pages = 5610–5637 | date = September 2011 | pmid = 21688848 | doi = 10.1021/cr100440g }}</ref><ref name=Patel2004b>{{cite journal | vauthors = Patel S, Mackerell AD, Brooks CL | title = CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model | journal = Journal of Computational Chemistry | volume = 25 | issue = 12 | pages = 1504–1514 | date = September 2004 | pmid = 15224394 | doi = 10.1002/jcc.20077 | s2cid = 16741310 | doi-access = free }}</ref> However, it is still uncertain how to best approximate polarizability in a simulation.{{Citation needed|date=April 2009}} The point becomes more important when a particle experiences different environments during its simulation trajectory, e.g. translocation of a drug through a cell membrane.<ref>{{cite journal | vauthors = Najla Hosseini A, Lund M, Ejtehadi MR | title = Electronic polarization effects on membrane translocation of anti-cancer drugs | journal = Physical Chemistry Chemical Physics | volume = 24 | issue = 20 | pages = 12281–12292 | date = May 2022 | pmid = 35543365 | doi = 10.1039/D2CP00056C | bibcode = 2022PCCP...2412281N | s2cid = 248696332 }}</ref>