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HandWiki. Potential Energy of Protein. Encyclopedia. Available online: https://encyclopedia.pub/entry/35901 (accessed on 21 September 2026).
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In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. All-atom force fields provide parameters for every type of atom in a system, including hydrogen, while united-atom interatomic potentials treat the hydrogen and carbon atoms in methyl groups and methylene bridges as one interaction center. Coarse-grained potentials, which are often used in long-time simulations of macromolecules such as proteins, nucleic acids, and multi-component complexes, sacrifice chemical details for higher computing efficiency.

macromolecules force field parameters multi-component

References

  1. "Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field". Langmuir 29 (6): 1754–65. February 2013. doi:10.1021/la3038846. PMID 23276161.  https://dx.doi.org/10.1021%2Fla3038846
  2. "Force Field for Mica-Type Silicates and Dynamics of Octadecylammonium Chains Grafted to Montmorillonite". Chemistry of Materials 17 (23): 5658–5669. November 2005. doi:10.1021/cm0509328. ISSN 0897-4756.  https://dx.doi.org/10.1021%2Fcm0509328
  3. Leach, Andrew (2001-01-30) (in en). Molecular Modelling: Principles and Applications (2nd ed.). Harlow: Prentice Hall. ISBN 9780582382107. 
  4. Sun, Huai; Mumby, Stephen J.; Maple, Jon R.; Hagler, Arnold T. (April 1994). "An ab Initio CFF93 All-Atom Force Field for Polycarbonates". Journal of the American Chemical Society 116 (7): 2978–2987. doi:10.1021/ja00086a030. ISSN 0002-7863.  https://dx.doi.org/10.1021%2Fja00086a030
  5. "CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data". Journal of Computational Chemistry 34 (25): 2135–45. September 2013. doi:10.1002/jcc.23354. PMID 23832629.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3800559
  6. "Development and testing of a general amber force field". Journal of Computational Chemistry 25 (9): 1157–74. July 2004. doi:10.1002/jcc.20035. PMID 15116359.  https://dx.doi.org/10.1002%2Fjcc.20035
  7. "A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution". Dalton Transactions 43 (27): 10602–16. July 2014. doi:10.1039/c4dt00438h. PMID 24828263.  https://dx.doi.org/10.1039%2Fc4dt00438h
  8. Gross, Kevin C.; Seybold, Paul G.; Hadad, Christopher M. (2002). "Comparison of different atomic charge schemes for predicting pKa variations in substituted anilines and phenols". International Journal of Quantum Chemistry 90 (1): 445–458. doi:10.1002/qua.10108. ISSN 0020-7608.  https://dx.doi.org/10.1002%2Fqua.10108
  9. "Modeling the Partial Atomic Charges in Inorganometallic Molecules and Solids and Charge Redistribution in Lithium-Ion Cathodes". Journal of Chemical Theory and Computation 10 (12): 5640–50. December 2014. doi:10.1021/ct500790p. PMID 26583247.  https://dx.doi.org/10.1021%2Fct500790p
  10. Heinz, Hendrik; Suter, Ulrich W. (November 2004). "Atomic Charges for Classical Simulations of Polar Systems". The Journal of Physical Chemistry B 108 (47): 18341–18352. doi:10.1021/jp048142t. ISSN 1520-6106. Bibcode: 2004APS..MAR.Y8006H.  https://dx.doi.org/10.1021%2Fjp048142t
  11. van Duin, Adri C. T.; Dasgupta, Siddharth; Lorant, Francois; Goddard, William A. (2001). "ReaxFF: A Reactive Force Field for Hydrocarbons". The Journal of Physical Chemistry A 105 (41): 9396–9409. doi:10.1021/jp004368u. Bibcode: 2001JPCA..105.9396V. http://www.wag.caltech.edu/publications/sup/pdf/471.pdf. 
  12. "Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system". Proteins 4 (1): 31–47. 1988. doi:10.1002/prot.340040106. PMID 3054871.  https://dx.doi.org/10.1002%2Fprot.340040106
  13. Dharmawardhana, Chamila C.; Kanhaiya, Krishan; Lin, Tzu-Jen; Garley, Amanda; Knecht, Marc R.; Zhou, Jihan; Miao, Jianwei; Heinz, Hendrik (2017-06-19). "Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF". Molecular Simulation 43 (13–16): 1394–1405. doi:10.1080/08927022.2017.1332414. ISSN 0892-7022.  https://dx.doi.org/10.1080%2F08927022.2017.1332414
  14. Liu, Juan; Tennessen, Emrys; Miao, Jianwei; Huang, Yu; Rondinelli, James M.; Heinz, Hendrik (2018-05-31). "Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations". The Journal of Physical Chemistry C 122 (26): 14996–15009. doi:10.1021/acs.jpcc.8b01891. ISSN 1932-7447.  https://dx.doi.org/10.1021%2Facs.jpcc.8b01891
  15. "Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials". The Journal of Physical Chemistry C 112 (44): 17281–17290. 2008-10-09. doi:10.1021/jp801931d. ISSN 1932-7447.  https://dx.doi.org/10.1021%2Fjp801931d
  16. Emami, Fateme S.; Puddu, Valeria; Berry, Rajiv J.; Varshney, Vikas; Patwardhan, Siddharth V.; Perry, Carole C.; Heinz, Hendrik (2014-04-02). "Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution". Chemistry of Materials 26 (8): 2647–2658. doi:10.1021/cm500365c. ISSN 0897-4756. http://irep.ntu.ac.uk/id/eprint/4652/1/4652_Perry.pdf. 
  17. "Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities". Chemical Society Reviews 45 (2): 412–48. January 2016. doi:10.1039/c5cs00890e. PMID 26750724.  https://dx.doi.org/10.1039%2Fc5cs00890e
  18. Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian (January 1996). "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids". Journal of the American Chemical Society 118 (45): 11225–11236. doi:10.1021/ja9621760. ISSN 0002-7863.  https://dx.doi.org/10.1021%2Fja9621760
  19. "UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations". Journal of the American Chemical Society 114 (25): 10024–10035. December 1992. doi:10.1021/ja00051a040. ISSN 0002-7863.  https://dx.doi.org/10.1021%2Fja00051a040
  20. "Theory of the Dielectric Constants of Alkali Halide Crystals". Physical Review 112 (1): 90–103. 1958-10-01. doi:10.1103/physrev.112.90. ISSN 0031-899X. Bibcode: 1958PhRv..112...90D.  https://dx.doi.org/10.1103%2Fphysrev.112.90
  21. "Shell model simulations by adiabatic dynamics". Journal of Physics: Condensed Matter 5 (8): 1031–1038. 1993-02-22. doi:10.1088/0953-8984/5/8/006. ISSN 0953-8984. Bibcode: 1993JPCM....5.1031M.  https://dx.doi.org/10.1088%2F0953-8984%2F5%2F8%2F006
  22. Yu, Haibo; van Gunsteren, Wilfred F. (November 2005). "Accounting for polarization in molecular simulation". Computer Physics Communications 172 (2): 69–85. doi:10.1016/j.cpc.2005.01.022. ISSN 0010-4655. Bibcode: 2005CoPhC.172...69Y.  https://dx.doi.org/10.1016%2Fj.cpc.2005.01.022
  23. "Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential". Nature Communications 9 (1): 716. February 2018. doi:10.1038/s41467-018-03137-8. PMID 29459638. Bibcode: 2018NatCo...9..716G.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5818522
  24. "CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations". Journal of Computational Chemistry 25 (1): 1–15. January 2004. doi:10.1002/jcc.10355. PMID 14634989.  https://dx.doi.org/10.1002%2Fjcc.10355
  25. Lin, Tzu-Jen; Heinz, Hendrik (2016-02-26). "Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces". The Journal of Physical Chemistry C 120 (9): 4975–4992. doi:10.1021/acs.jpcc.5b12504. ISSN 1932-7447.  https://dx.doi.org/10.1021%2Facs.jpcc.5b12504
  26. "An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications". Chemical Reviews 116 (9): 4983–5013. May 2016. doi:10.1021/acs.chemrev.5b00505. PMID 26815602.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4865892
  27. Lorentz, Hendrik A. (1905). "The Motion of Electrons in Metallic Bodies, I.". Proc. K. Ned. Akad. Wet. 7: 451. Bibcode: 1904KNAB....7..438L.  http://adsabs.harvard.edu/abs/1904KNAB....7..438L
  28. Drude, Paul (1900). "Zur Elekronentheorie der Metalle. I. Teil.". Annalen der Physik 306 (3): 566–613. doi:10.1002/andp.19003060312. https://zenodo.org/record/1423977. 
  29. "Optimization of the OPLS-AA Force Field for Long Hydrocarbons". Journal of Chemical Theory and Computation 8 (4): 1459–70. April 2012. doi:10.1021/ct200908r. PMID 26596756.  https://dx.doi.org/10.1021%2Fct200908r
  30. "AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA". Journal of Chemical Theory and Computation 3 (4): 1464–75. July 2007. doi:10.1021/ct600329w. PMID 26633217.  https://dx.doi.org/10.1021%2Fct600329w
  31. "A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation". Journal of Chemical Theory and Computation 8 (11): 4719–31. November 2012. doi:10.1021/ct300534j. PMID 26605626.  https://dx.doi.org/10.1021%2Fct300534j
  32. "Building Force Fields: An Automatic, Systematic, and Reproducible Approach". The Journal of Physical Chemistry Letters 5 (11): 1885–91. June 2014. doi:10.1021/jz500737m. PMID 26273869.  https://dx.doi.org/10.1021%2Fjz500737m
  33. "Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields". Journal of Chemical Information and Modeling 59 (10): 4278–4288. October 2019. doi:10.1021/acs.jcim.9b00646. PMID 31549507.  https://dx.doi.org/10.1021%2Facs.jcim.9b00646
  34. Emami, Fateme S.; Puddu, Valeria; Berry, Rajiv J.; Varshney, Vikas; Patwardhan, Siddharth V.; Perry, Carole C.; Heinz, Hendrik (2014-04-22). "Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution". Chemistry of Materials 26 (8): 2647–2658. doi:10.1021/cm500365c. ISSN 0897-4756. http://irep.ntu.ac.uk/id/eprint/4652/1/4652_Perry.pdf. 
  35. Ruiz, Victor G.; Liu, Wei; Tkatchenko, Alexandre (2016-01-15). "Density-functional theory with screened van der Waals interactions applied to atomic and molecular adsorbates on close-packed and non-close-packed surfaces". Physical Review B 93 (3): 035118. doi:10.1103/physrevb.93.035118. ISSN 2469-9950. Bibcode: 2016PhRvB..93c5118R.  https://dx.doi.org/10.1103%2Fphysrevb.93.035118
  36. "Density-functional theory with screened van der Waals interactions for the modeling of hybrid inorganic-organic systems". Physical Review Letters 108 (14): 146103. April 2012. doi:10.1103/physrevlett.108.146103. PMID 22540809. Bibcode: 2012PhRvL.108n6103R.  https://dx.doi.org/10.1103%2Fphysrevlett.108.146103
  37. "Charge Anisotropy: Where Atomic Multipoles Matter Most". Journal of Chemical Theory and Computation 10 (10): 4488–96. October 2014. doi:10.1021/ct5005565. PMID 26588145.  https://dx.doi.org/10.1021%2Fct5005565
  38. Mahoney, Michael W.; Jorgensen, William L. (2000-05-22). "A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions". The Journal of Chemical Physics 112 (20): 8910–8922. doi:10.1063/1.481505. ISSN 0021-9606. Bibcode: 2000JChPh.112.8910M.  https://dx.doi.org/10.1063%2F1.481505
  39. "Three-dimensional coordinates of individual atoms in materials revealed by electrontomography". Nature Materials 14 (11): 1099–103. November 2015. doi:10.1038/nmat4426. PMID 26390325. Bibcode: 2015NatMa..14.1099X.  https://dx.doi.org/10.1038%2Fnmat4426
  40. "Carbon Nanotube Dispersion in Solvents and Polymer Solutions: Mechanisms, Assembly, and Preferences". ACS Nano 11 (12): 12805–12816. December 2017. doi:10.1021/acsnano.7b07684. PMID 29179536.  https://dx.doi.org/10.1021%2Facsnano.7b07684
  41. "Interatomic potentials and solvation parameters from protein engineering data for buried residues". Protein Science 11 (8): 1984–2000. August 2002. doi:10.1110/ps.0307002. PMID 12142453.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2373680
  42. "Modeling electrostatic effects in proteins". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1764 (11): 1647–76. November 2006. doi:10.1016/j.bbapap.2006.08.007. PMID 17049320.  https://dx.doi.org/10.1016%2Fj.bbapap.2006.08.007
  43. "What are the dielectric "constants" of proteins and how to validate electrostatic models?". Proteins 44 (4): 400–17. September 2001. doi:10.1002/prot.1106. PMID 11484218.  https://dx.doi.org/10.1002%2Fprot.1106
  44. "Intermolecular and Surface Forces". Elsevier. 2011. pp. iii. doi:10.1016/b978-0-12-391927-4.10024-6. ISBN 978-0-12-391927-4.  https://dx.doi.org/10.1016%2Fb978-0-12-391927-4.10024-6
  45. "Intermolecular forces in biology". Quarterly Reviews of Biophysics 34 (2): 105–267. May 2001. doi:10.1017/S0033583501003687. PMID 11771120.  https://dx.doi.org/10.1017%2FS0033583501003687
  46. "Polyacrylonitrile Interactions with Carbon Nanotubes in Solution: Conformations and Binding as a Function of Solvent, Temperature, and Concentration". Advanced Functional Materials 29 (50): 1905247. 2019-10-03. doi:10.1002/adfm.201905247. ISSN 1616-301X.  https://dx.doi.org/10.1002%2Fadfm.201905247
  47. "A brighter future for protein structure prediction". Nature Structural Biology 6 (2): 108–11. February 1999. doi:10.1038/5794. PMID 10048917.  https://dx.doi.org/10.1038%2F5794
  48. "Molecular dynamics applied to X-ray structure refinement". Accounts of Chemical Research 35 (6): 404–12. June 2002. doi:10.1021/ar010034r. PMID 12069625.  https://dx.doi.org/10.1021%2Far010034r
  49. "Structure calculation of biological macromolecules from NMR data". Quarterly Reviews of Biophysics 31 (2): 145–237. May 1998. doi:10.1017/S0033583598003436. PMID 9794034.  https://dx.doi.org/10.1017%2FS0033583598003436
  50. Ostermeir, Katja; Zacharias, Martin (January 2013). "163 Enhanced sampling of peptides and proteins with a new biasing replica exchange method". Journal of Biomolecular Structure and Dynamics 31 (sup1): 106. doi:10.1080/07391102.2013.786405. ISSN 0739-1102.  https://dx.doi.org/10.1080%2F07391102.2013.786405
  51. "Assessment of homology-based predictions in CASP5". Proteins 53 Suppl 6: 352–68. 2003. doi:10.1002/prot.10543. PMID 14579324.  https://dx.doi.org/10.1002%2Fprot.10543
  52. "Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors". Angewandte Chemie 41 (15): 2644–76. August 2002. doi:10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O. PMID 12203463.  https://dx.doi.org/10.1002%2F1521-3773%2820020802%2941%3A15%3C2644%3A%3AAID-ANIE2644%3E3.0.CO%3B2-O
  53. "Structural energetics of protein folding and binding". Current Opinion in Biotechnology 11 (1): 62–6. February 2000. doi:10.1016/s0958-1669(99)00055-5. PMID 10679345.  https://dx.doi.org/10.1016%2Fs0958-1669%2899%2900055-5
  54. "Effective energy functions for protein structure prediction". Current Opinion in Structural Biology 10 (2): 139–45. April 2000. doi:10.1016/s0959-440x(00)00063-4. PMID 10753811.  https://dx.doi.org/10.1016%2Fs0959-440x%2800%2900063-4
  55. Javidpour, Leili (2012). "Computer Simulations of Protein Folding". Computing in Science & Engineering 14 (2): 97–103. doi:10.1109/MCSE.2012.21. Bibcode: 2012CSE....14b..97J.  https://dx.doi.org/10.1109%2FMCSE.2012.21
  56. "Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8". Proteins 77 Suppl 9: 114–22. 2009. doi:10.1002/prot.22570. PMID 19768677.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2922016
  57. "Energy functions for protein design". Current Opinion in Structural Biology 9 (4): 509–13. August 1999. doi:10.1016/S0959-440X(99)80072-4. PMID 10449371.  https://dx.doi.org/10.1016%2FS0959-440X%2899%2980072-4
  58. "Energy estimation in protein design". Current Opinion in Structural Biology 12 (4): 441–6. August 2002. doi:10.1016/s0959-440x(02)00345-7. PMID 12163065.  https://dx.doi.org/10.1016%2Fs0959-440x%2802%2900345-7
  59. Rohl, Carol A.; Strauss, Charlie E.M.; Misura, Kira M.S.; Baker, David (2004). "Protein Structure Prediction Using Rosetta". Numerical Computer Methods, Part D. Methods in Enzymology. 383. pp. 66–93. doi:10.1016/S0076-6879(04)83004-0. ISBN 9780121827885.  https://dx.doi.org/10.1016%2FS0076-6879%2804%2983004-0
  60. "Positioning of proteins in membranes: a computational approach". Protein Science 15 (6): 1318–33. June 2006. doi:10.1110/ps.062126106. PMID 16731967.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2242528
  61. "Solid model compounds and the thermodynamics of protein unfolding". Journal of Molecular Biology 222 (3): 699–709. December 1991. doi:10.1016/0022-2836(91)90506-2. PMID 1660931.  https://dx.doi.org/10.1016%2F0022-2836%2891%2990506-2
  62. "Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition". Biopolymers 28 (10): 1667–80. October 1989. doi:10.1002/bip.360281003. PMID 2597723.  https://dx.doi.org/10.1002%2Fbip.360281003
  63. "Thermodynamic stability of globular proteins: a reliable model from small molecule studies". Gazetta Chim. Italiana 126: 559–567. 1996. 
  64. "Hydrogen bonding stabilizes globular proteins". Biophysical Journal 71 (4): 2033–9. October 1996. doi:10.1016/S0006-3495(96)79401-8. PMID 8889177. Bibcode: 1996BpJ....71.2033M.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1233669
  65. "Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water". Proceedings of the National Academy of Sciences of the United States of America 88 (7): 2854–8. April 1991. doi:10.1073/pnas.88.7.2854. PMID 2011594. Bibcode: 1991PNAS...88.2854S.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=51338
  66. "Geometry of the intermolecular XH. cntdot.. cntdot.. cntdot. Y (X, Y= N, O) hydrogen bond and the calibration of empirical hydrogen-bond potentials.". The Journal of Physical Chemistry 98 (18): 4831–7. May 1994. doi:10.1021/j100069a010.  https://dx.doi.org/10.1021%2Fj100069a010
  67. "Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms.". Journal of the American Chemical Society 99 (25): 8127–34. December 1977. doi:10.1021/ja00467a001.  https://dx.doi.org/10.1021%2Fja00467a001
  68. "MM2 and MM3 home page". http://europa.chem.uga.edu/allinger/mm2mm3.html. 
  69. "Molecular mechanics. The MM3 force field for hydrocarbons. 1.". Journal of the American Chemical Society 111 (23): 8551–66. November 1989. doi:10.1021/ja00205a001.  https://dx.doi.org/10.1021%2Fja00205a001
  70. "Molecular mechanics. The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics.". Journal of the American Chemical Society 111 (23): 8566–75. November 1989. doi:10.1021/ja00205a002.  https://dx.doi.org/10.1021%2Fja00205a002
  71. "Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons.". Journal of the American Chemical Society 111 (23): 8576–82. November 1989. doi:10.1021/ja00205a003.  https://dx.doi.org/10.1021%2Fja00205a003
  72. "The program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space.". Biopolymers 29 (4–5): 679–94. March 1990. doi:10.1002/bip.360290403.  https://dx.doi.org/10.1002%2Fbip.360290403
  73. "Interface Force Field (IFF)". Heinz Laboratory. 2 February 2016. https://bionanostructures.com/interface-md/. 
  74. Mishra, Ratan K.; Mohamed, Aslam Kunhi; Geissbühler, David; Manzano, Hegoi; Jamil, Tariq; Shahsavari, Rouzbeh; Kalinichev, Andrey G.; Galmarini, Sandra et al. (December 2017). "A force field database for cementitious materials including validations, applications and opportunities". Cement and Concrete Research 102: 68–89. doi:10.1016/j.cemconres.2017.09.003. http://hal.in2p3.fr/in2p3-01633100/file/Mishra-CEMCON_2017-accepted.pdf. 
  75. "Molecular mechanics with fluctuating atomic charges–a new force field with a semi-empirical charge calculation.". Molecular Modeling Annual 7 (4): 90–102. May 2001. doi:10.1007/s008940100008.  https://dx.doi.org/10.1007%2Fs008940100008
  76. "ECEPP". https://biohpc.cornell.edu/software/eceppak/README.html. 
  77. "Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids.". The Journal of Physical Chemistry 79 (22): 2361–81. October 1975. doi:10.1021/j100589a006.  https://dx.doi.org/10.1021%2Fj100589a006
  78. "A new force field (ECEPP-05) for peptides, proteins, and organic molecules". The Journal of Physical Chemistry B 110 (10): 5025–44. March 2006. doi:10.1021/jp054994x. PMID 16526746.  https://dx.doi.org/10.1021%2Fjp054994x
  79. "GROMOS". https://www.igc.ethz.ch/gromos.html. 
  80. "Quantum mechanical consistent force field (QCFF/PI) method: Calculations of energies, conformations and vibronic interactions of ground and excited states of conjugated molecules.". Israel Journal of Chemistry 11 (5): 709–17. 1973. doi:10.1002/ijch.197300067.  https://dx.doi.org/10.1002%2Fijch.197300067
  81. QCFF/PI: A Program for the Consistent Force Field Evaluation of Equilibrium Geometries and Vibrational Frequencies of Molecules (Report). Indiana University: Quantum Chemistry Program Exchange. 1974. p. QCPE 247. 
  82. "New-generation amber united-atom force field". The Journal of Physical Chemistry B 110 (26): 13166–76. July 2006. doi:10.1021/jp060163v. PMID 16805629.  https://dx.doi.org/10.1021%2Fjp060163v
  83. "Tinker Molecular Modeling Package". https://dasher.wustl.edu/tinker/. 
  84. "Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential". The Journal of Physical Chemistry Letters 11 (2): 419–426. January 2020. doi:10.1021/acs.jpclett.9b03489. PMID 31865706.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=7384396
  85. "AMOEBA+ Classical Potential for Modeling Molecular Interactions". Journal of Chemical Theory and Computation 15 (7): 4122–4139. July 2019. doi:10.1021/acs.jctc.9b00261. PMID 31136175.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=6615954
  86. "CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model". Journal of Computational Chemistry 25 (12): 1504–14. September 2004. doi:10.1002/jcc.20077. PMID 15224394.  https://dx.doi.org/10.1002%2Fjcc.20077
  87. "Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator". Journal of Chemical Theory and Computation 1 (1): 153–68. January 2005. doi:10.1021/ct049930p. PMID 26641126.  https://dx.doi.org/10.1021%2Fct049930p
  88. "Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field". Journal of Chemical Theory and Computation 6 (3): 774–786. 2010. doi:10.1021/ct900576a. PMID 20300554.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2838399
  89. "Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme". Journal of Molecular Biology 103 (2): 227–49. May 1976. doi:10.1016/0022-2836(76)90311-9. PMID 985660.  https://dx.doi.org/10.1016%2F0022-2836%2876%2990311-9
  90. "New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems.". Journal of Computational Chemistry 15 (5): 524–31. May 1994. doi:10.1002/jcc.540150505.  https://dx.doi.org/10.1002%2Fjcc.540150505
  91. "DRF90: a polarizable force field.". Molecular Simulation 32 (6): 471–84. May 2006. doi:10.1080/08927020600631270.  https://dx.doi.org/10.1080%2F08927020600631270
  92. "Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations". Chemical Reviews 100 (11): 4087–108. November 2000. doi:10.1021/cr9900477. PMID 11749341.  https://dx.doi.org/10.1021%2Fcr9900477
  93. "A polarizable intermolecular potential function for simulation of liquid alcohols.". The Journal of Physical Chemistry 99 (44): 16460–7. November 1995. doi:10.1021/j100044a039.  https://dx.doi.org/10.1021%2Fj100044a039
  94. "Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes". Journal of Chemical Theory and Computation 3 (6): 1878–1889. 2007. doi:10.1021/ct700146x. PMID 18958290.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2572772
  95. "A Polarizable Force Field and Continuum Solvation Methodology for Modeling of Protein-Ligand Interactions". Journal of Chemical Theory and Computation 1 (4): 694–715. July 2005. doi:10.1021/ct049855i. PMID 26641692.  https://dx.doi.org/10.1021%2Fct049855i
  96. "A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle.". The Journal of Chemical Physics 117 (20): 9175–89. November 2002. doi:10.1063/1.1515773. Bibcode: 2002JChPh.117.9175C.  https://dx.doi.org/10.1063%2F1.1515773
  97. "A Polarizable and Transferable PHAST N2 Potential for Use in Materials Simulation". Journal of Chemical Theory and Computation 9 (12): 5550–7. December 2013. doi:10.1021/ct400526a. PMID 26592288.  https://dx.doi.org/10.1021%2Fct400526a
  98. "Anthony Stone: Computer programs". http://www-stone.ch.cam.ac.uk/programs.html. 
  99. "Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy". Journal of Chemical Theory and Computation 3 (6): 1960–1986. November 2007. doi:10.1021/ct700134r. PMID 18978934.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2367138
  100. "Towards a force field based on density fitting". The Journal of Chemical Physics 124 (10): 104101. March 2006. doi:10.1063/1.2173256. PMID 16542062. Bibcode: 2006JChPh.124j4101P.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2080832
  101. "Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods". The Journal of Chemical Physics 125 (18): 184101. November 2006. doi:10.1063/1.2363374. PMID 17115732. Bibcode: 2006JChPh.125r4101C.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2080839
  102. "Polarizable force field development and molecular dynamics simulations of ionic liquids". The Journal of Physical Chemistry B 113 (33): 11463–78. August 2009. doi:10.1021/jp905220k. PMID 19637900.  https://dx.doi.org/10.1021%2Fjp905220k
  103. "Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems". Angewandte Chemie International Edition 59 (36): 15665–15673. September 2020. doi:10.1002/anie.202004239. PMID 32343883.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=7267649
  104. "Simulating Microscopic Hydrodynamic Phenomena with Dissipative Particle Dynamics". Europhysics Letters (EPL) 19 (3): 155–160. 1992. doi:10.1209/0295-5075/19/3/001. ISSN 0295-5075. Bibcode: 1992EL.....19..155H.  https://dx.doi.org/10.1209%2F0295-5075%2F19%2F3%2F001
  105. "Dynamic Simulations of Hard-Sphere Suspensions Under Steady Shear". Europhysics Letters (EPL) 21 (3): 363–368. 1993. doi:10.1209/0295-5075/21/3/018. ISSN 0295-5075. Bibcode: 1993EL.....21..363K.  https://dx.doi.org/10.1209%2F0295-5075%2F21%2F3%2F018
  106. "Statistical Mechanics of Dissipative Particle Dynamics". Europhysics Letters (EPL) 30 (4): 191–196. 1995. doi:10.1209/0295-5075/30/4/001. ISSN 0295-5075. Bibcode: 1995EL.....30..191E.  https://dx.doi.org/10.1209%2F0295-5075%2F30%2F4%2F001
  107. Dissipative Particle Dynamics: Addressing deficiencies and establishing new frontiers, CECAM workshop, July 16–18, 2008, Lausanne, Switzerland. http://www.cecam.org/workshop-0-188.html
  108. "The MARTINI force field: coarse grained model for biomolecular simulations". The Journal of Physical Chemistry B 111 (27): 7812–24. July 2007. doi:10.1021/jp071097f. PMID 17569554. https://pure.rug.nl/ws/files/6707449/2007JPhysChemBMarrink.pdf. 
  109. "SAFT". http://molecularsystemsengineering.org/saft.html. 
  110. "A force field for virtual atom molecular mechanics of proteins". Proceedings of the National Academy of Sciences of the United States of America 106 (37): 15667–72. September 2009. doi:10.1073/pnas.0907674106. PMID 19717427. Bibcode: 2009PNAS..10615667K.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2734882
  111. "ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost". Chemical Science 8 (4): 3192–3203. April 2017. doi:10.1039/C6SC05720A. PMID 28507695.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5414547
  112. "Description of Potential Energy Surfaces of Molecules Using FFLUX Machine Learning Models". Journal of Chemical Theory and Computation 15 (1): 116–126. January 2019. doi:10.1021/acs.jctc.8b00806. PMID 30507180.  https://dx.doi.org/10.1021%2Facs.jctc.8b00806
  113. "Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning". Journal of Chemical Theory and Computation 12 (6): 2742–51. June 2016. doi:10.1021/acs.jctc.6b00457. PMID 27224739.  https://dx.doi.org/10.1021%2Facs.jctc.6b00457
  114. "Machine Learning of Dynamic Electron Correlation Energies from Topological Atoms". Journal of Chemical Theory and Computation 14 (1): 216–224. January 2018. doi:10.1021/acs.jctc.7b01157. PMID 29211469.  https://dx.doi.org/10.1021%2Facs.jctc.7b01157
  115. "Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach". Journal of Chemical Theory and Computation 11 (5): 2087–96. May 2015. doi:10.1021/acs.jctc.5b00099. PMID 26574412. Bibcode: 2015arXiv150304987R.  https://dx.doi.org/10.1021%2Facs.jctc.5b00099
  116. "SchNet - A deep learning architecture for molecules and materials". The Journal of Chemical Physics 148 (24): 241722. June 2018. doi:10.1063/1.5019779. PMID 29960322. Bibcode: 2018JChPh.148x1722S.  https://dx.doi.org/10.1063%2F1.5019779
  117. O. T. Unke and M. Meuwly (2019). "PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges". J. Chem. Theo. Chem. 15 (6): 3678–3693. doi:10.1021/acs.jctc.9b00181. PMID 31042390.  https://dx.doi.org/10.1021%2Facs.jctc.9b00181
  118. "A general purpose model for the condensed phases of water: TIP4P/2005". The Journal of Chemical Physics 123 (23): 234505. December 2005. doi:10.1063/1.2121687. PMID 16392929. Bibcode: 2005JChPh.123w4505A.  https://dx.doi.org/10.1063%2F1.2121687
  119. "Water modeled as an intermediate element between carbon and silicon". The Journal of Physical Chemistry B 113 (13): 4008–16. April 2009. doi:10.1021/jp805227c. PMID 18956896.  https://dx.doi.org/10.1021%2Fjp805227c
  120. "A FFLUX Water Model: Flexible, Polarizable and with a Multipolar Description of Electrostatics". Journal of Computational Chemistry 41 (7): 619–628. March 2020. doi:10.1002/jcc.26111. PMID 31747059.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=7004022
  121. "Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications". Journal of Chemical Theory and Computation 9 (12): 5653–5674. December 2013. doi:10.1021/ct400556v. PMID 24489522.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3904396
  122. "Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family". ACS Synthetic Biology 3 (12): 855–69. December 2014. doi:10.1021/sb400168u. PMID 24932669.  http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4277759
  123. "Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models". Computers & Chemical Engineering 71: 745–752. 2014. doi:10.1016/j.compchemeng.2014.07.017.  https://dx.doi.org/10.1016%2Fj.compchemeng.2014.07.017
  124. Deeth, Robert J. (2001). "The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons". Coordination Chemistry Reviews 212 (212): 11–34. doi:10.1016/S0010-8545(00)00354-4.  https://dx.doi.org/10.1016%2FS0010-8545%2800%2900354-4
  125. "Integration of Ligand Field Molecular Mechanics in Tinker". Journal of Chemical Information and Modeling 55 (6): 1282–90. June 2015. doi:10.1021/acs.jcim.5b00098. PMID 25970002.  https://dx.doi.org/10.1021%2Facs.jcim.5b00098
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