Editing Molecular dynamics (section)

=== Empirical potentials ===

Empirical potentials used in chemistry are frequently called [[Force field (chemistry)|force fields]], while those used in materials physics are called [[interatomic potential]]s.

Most [[Force field (chemistry)|force fields]] in chemistry are empirical and consist of a summation of bonded forces associated with [[chemical bond]]s, bond angles, and bond [[dihedral angle|dihedrals]], and non-bonded forces associated with [[van der Waals force]]s and [[electrostatic charge]].<ref>{{cite journal | vauthors = Rizzuti B | title = Molecular simulations of proteins: From simplified physical interactions to complex biological phenomena | journal =   Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics| year = 2022 | volume = 1870 | issue = 3 | pages = 140757 | pmid = 35051666 | doi = 10.1016/j.bbapap.2022.140757 | s2cid = 263455009 }}</ref> Empirical potentials represent quantum-mechanical effects in a limited way through ad hoc functional approximations. These potentials contain free parameters such as [[electrostatic charge|atomic charge]], van der Waals parameters reflecting estimates of [[atomic radius]], and equilibrium [[bond length]], angle, and dihedral; these are obtained by fitting against detailed electronic calculations (quantum chemical simulations) or experimental physical properties such as [[Young's modulus|elastic constants]], lattice parameters and [[spectroscopy|spectroscopic]] measurements.

Because of the non-local nature of non-bonded interactions, they involve at least weak interactions between all particles in the system. Its calculation is normally the bottleneck in the speed of MD simulations. To lower the computational cost, [[Force field (chemistry)|force fields]] employ numerical approximations such as shifted cutoff radii, [[reaction field method|reaction field]] algorithms, particle mesh [[Ewald summation]], or the newer particle–particle-particle–mesh ([[P3M]]).

Chemistry force fields commonly employ preset bonding arrangements (an exception being ''[[ab initio quantum chemistry methods|ab initio]]'' dynamics), and thus are unable to model the process of chemical bond breaking and reactions explicitly. On the other hand, many of the potentials used in physics, such as those based on the [[bond order potential|bond order formalism]] can describe several different coordinations of a system and bond breaking.<ref>{{cite journal | vauthors = Sinnott SB, Brenner DW |author-link1=Susan Sinnott|year= 2012 |title= Three decades of many-body potentials in materials research |journal= MRS Bulletin |volume= 37 |issue= 5 |pages= 469–473 |doi=10.1557/mrs.2012.88|doi-access= free |bibcode=2012MRSBu..37..469S }}</ref><ref>{{cite journal | vauthors = Albe K, Nordlund K, Averback RS |year= 2002 |title= Modeling metal-semiconductor interaction: Analytical bond-order potential for platinum-carbon |journal= Phys. Rev. B |volume= 65 |issue= 19 |page= 195124 |doi=10.1103/physrevb.65.195124|bibcode= 2002PhRvB..65s5124A}}</ref> Examples of such potentials include the [[Brenner potential]]<ref>{{cite journal | vauthors = Brenner DW | title = Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films | journal = Physical Review B | volume = 42 | issue = 15 | pages = 9458–9471 | date = November 1990 | pmid = 9995183 | doi = 10.1103/physrevb.42.9458 | url = https://apps.dtic.mil/sti/pdfs/ADA230023.pdf | url-status = live | bibcode = 1990PhRvB..42.9458B | archive-url = https://web.archive.org/web/20170922092328/http://www.dtic.mil/get-tr-doc/pdf?AD=ADA230023 | archive-date = September 22, 2017 }}</ref> for hydrocarbons and its
further developments for the C-Si-H<ref>{{cite journal|doi=10.1080/01418619608240734|title= Empirical potentials for C-Si-H systems with application to C<sub>60</sub> interactions with Si crystal surfaces|journal= Philosophical Magazine A|volume= 74|issue= 6|pages= 1439–1466|year= 1996| vauthors = Beardmore K, Smith R |bibcode= 1996PMagA..74.1439B}}</ref> and C-O-H<ref>{{cite journal|title=A reactive empirical bond order (rebo) potential for hydrocarbon oxygen interactions|journal=Journal of Physics: Condensed Matter|volume=16|issue=41|pages=7261–7275|doi=10.1088/0953-8984/16/41/008|year=2004| vauthors = Ni B, Lee KH, Sinnott SB |bibcode= 2004JPCM...16.7261N|s2cid=250760409 }}</ref> systems. The [[ReaxFF]] potential<ref>{{cite journal | vauthors = Van Duin AC, Dasgupta S, Lorant F, Goddard WA |title=ReaxFF: A Reactive Force Field for Hydrocarbons |journal=The Journal of Physical Chemistry A |date=October 2001 |volume=105 |issue=41 |pages=9396–9409 |doi=10.1021/jp004368u |bibcode= 2001JPCA..105.9396V |citeseerx=10.1.1.507.6992}}</ref> can be considered a fully reactive hybrid between bond order potentials and chemistry force fields.