ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces

Journal of Computational Chemistry

Volumn 31, Issue 12, 2010, Pages 2307-2316

  Waldher, Benjamin ^a   Kuta, Jadwiga ^a   Chen, Samuel ^a   Henson, Neil ^b   Clark, Aurora E ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Force field; Force matching; Potential energy surfaces

Indexed keywords

CLASSICAL FORCE FIELDS; CODE DESIGNS; ENERGY SURFACE; FORCE FIELDS; FORCE MATCHING; FORCE-MATCHING ALGORITHM; FUNCTIONAL FORCES; LEAST SQUARES MINIMIZATION; NON-PROPRIETARY PLATFORMS; PROGRAM PACKAGES; QUANTUM MECHANICAL; QUANTUM MECHANICAL POTENTIAL; REFERENCE DATA; TEMPLATED;

ELECTRONIC STRUCTURE; GRAPHICAL USER INTERFACES; OPTIMIZATION; POTENTIAL ENERGY; QUANTUM CHEMISTRY; SOFTWARE PACKAGES; SURFACE PHENOMENA;

POTENTIAL ENERGY SURFACES;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; ELECTROMAGNETIC FIELD; ENERGY TRANSFER; FACTUAL DATABASE; QUANTUM THEORY; REGRESSION ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, FACTUAL; ELECTROMAGNETIC FIELDS; ENERGY TRANSFER; LEAST-SQUARES ANALYSIS; MODELS, MOLECULAR; QUANTUM THEORY; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77956245192     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21523     Document Type: Article

References (48)

1. Halgren, T. A. J Am Chem Soc 1992, 114, 7827.
2. Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J Am Chem Soc 1992, 114, 10024.
3. Badger, R. M. J Chem. Phys 1935, 3, 710.
4. Cygan, R. T.; Liang, J.-J.; Kalinichev, A. G. J Phys Chem B 2004, 108, 1255.
5. Norrby, P.-O.; Liljefors, T. J. Comp Chem .1998, 19, 1146.
6. Cornell, W.D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
7. Brooks, B. R.; Bruccoleri R.E.; Olafson B.D.; States D.J.; Swaminathan S.; Karplus, M, J Comp Chem 1983, 4, 187.
8. MacKerell, A. D., Jr.; Brooks, B.; Brooks, C. L., III; Nilsson, L.; Roux, B.; Won, Y.; Karplus, M.; in The Encyclopedia of Computational Chemistry, Vol. 1.; Schleyer, P. V. R.; Schreiner, P. R.; Allinger, N. L.; Clark. T.; Gasteiger, J.; Kollman, P.; Schaefer, H. F., III, eds. Wiley: Chicester 1998; pp. 271-277.
9. Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. G.; Wolff, J.; Genest, M., Hagler, A. T. Proteins 1988, 4, 31.
10. Jorgensen, W. L.; Tirado-Rives, J. J Am Chem Soc 1988, 110, 1657.
11. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J Am Chem Soc 1996, 118, 11225.
12. Ponder, J. A.; Case, D. A. Adv Protein Chem. 2003, 66, 27.
13. Maple, J. R.; Dinur, U.; Hagler, A. T. Proc Natl Acad Sci USA 1988, 85, 5350.
14. Maple, J. R.; Hwang, M.-J.; Stockfisch, T. P.; Dinur, U.; Waldman, M.; Ewig, C. S.; Hagler, A. T. J Comp Chem 1994, 15, 162.
15. Engvist, O.; Astrancl, P.-O.; Karlstrom G. Chem Rev 2000, 100, 4087.
16. Hwang, M. J.; Stockfisch, T. P.; Hagler, A. T. J Am Chem Soc 1994, 116, 2515.
17. Jaffe, R. L.; Smith, G. D.; Yoon, D. Y. J Phys Chem 1993, 97, 12745.
18. Smith, G. D.; Jaffe, R. L.; Yoon, D. Y. J Phys Chem 1993, 97, 12752.
19. Smith, G. D.; Jaffe, R. L.; Yoon, D. Y. J Am Chem Soc 1995, 117, 530.
20. Smith, G. D.; Borodin, O.; Pekny, M.; Annis, B.; Londono, D.; Jaffe, R. L. Spectochim Acta A 1997, 53, 1273.
21. Hagberg, D.; Bednarz, E.; Edelstein, N. M.; Gagliardi, L. J Am Chem Soc 2007, 129, 14136.
22. Nielson, K. D.; van. Duin, A. C. T.; Oxgaard, J.; Deng, W. -Q.; Goddard, W. A., III. J Phys Chem A 2005, 109, 493.
23. Guvench, O.; MacKerell, A. D., Jr. J Mol Model 2008, 14, 667.
24. Vaiana, A. C.; Cournia, Z.; Costescu, I. B.; Smith, J. C. Comp Phys Comui 2005, 167, 34.
25. Globus, A.; Langhirt, E.; Livny, M.; Ramamurthy, R.; Solomon, M.; Traugott, S.JavaGenes and condor: Cycle-scavenging genetic algorithms, Java Grande 2000, sponsored by ACM. SIGPLAN, San Francisco, CA, June 3-4, 2000.
26. Available through Aeon technology at: http://www.aeo.ntechno.logy. com/
27. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Kiene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian. 03, Revision C. 02, Gaussian, Inc.: Wallingford, CT, 2004.
28. Bylaska, E. J.; de Jong, W. A,; Kowalski, K.; Straatsma, T. P.; Valiev, M.; Wang, D.; E.Aprà, Windus, T. L.; Hirata, S.; Hackler, M. T.; Zhao, Y.; P.-Fan, D.; Harrison, R. J.; Dupuis, M.; Smith, D. M. A.; Nieplocha, J.; Tipparaju, V.; Krishnan, M.; Auer, A. A.; Nooijen, M.; Brown, E,; Cisneros, G.; Fann, G. I.; H.Früchtl, Garza, J.; Hirao, K.; Kendall, R.; Nichols, J. A.; Tsemekhman, K.; Wolinski, K.; Anchell, J.; Bernholdt, D.; Borowski, P.; Clark, T.; Clerc, D.; Dachsel, H.; Deegan, M.; Dyall, K.; Elwood, D.; Glendening, E.; Gutowski, M.; Hess, A.; Jaffe, J.; Johnson, B.; Ju, J.; Kobayashi, R.; Kutteh, R.; Lin, Z.; Littlefielcl, R.; Long, X.; Meng, B.; Nakajima, T.; Niu, S.; Pollack, L.; Rosing, M.; Sandrone, G.; Stave, M.; Taylor, H.; Thomas, G.; J.van Lenthe, Wong, A.; Zhang, Z. NWChem, A. Computational Chemistry Package for Parallel Computers, Version 5.0; Pacific Northwest National. Laboratory: Richland, WA, 2006.
29. Smith, W. Mol. Sim 2006, 32, 933-1121. Available at: www.ccp5.ac.uk/DL- POLY/.
30. Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 1.0, University of California, San. Francisco, 2008.
31. Plimpton, S. J. J Comp Phys 1995, 1171-19. Available at: http://lammps.sandia.gov.
32. Powell, M. J. D. Comput J 1965, 7, 303.
33. Available at: http://www.gtk.org.
34. Urey, H. C.; Bradley, C. A. Phys Rev 1931, 38, 1969.
35. Lennard-Jones, J. E. Proc R Soc Lond A 1924, 106, 463.
36. Ren, P. Y.; Ponder, J. W. J Comp Chem 2002, 23, 1497.
37. Ren, P. Y.; Ponder, J. W. J Phys Chem B 2003, 107, 5933.
38. Ren, P. Y.; Ponder, J. W. J. Phys. Chem. B. 2004, 108, 13427.
39. Schnieders, M, J.; Baker, N. A.; Ren, P. Y.; Ponder, J. W. J Chem Phys 2007, 126, 124114.
40. Schnieders, M. J.; Ponder, J. W. J Chem Theory Comput 2007, 3, 2083.
41. Ercoiessi, F.; Adams, J. B. Europhys Lett 1994, 26, 583.
42. Lopez, M. J.; Jellinek, J. J Chem Phys 1999, 110, 8899.
43. Press, W. H.; Teukolsky, S. A.; Vetterung, W. T.; Flannery, B. P. Numerical. Recipes in C: The Art of Scientific Computing, 2nd ed.; Cambridge University Press: Cambridge, 1992.
44. Teleman, O.; Jonsson, B.; Engstrom, S. Mol Phys 1987, 60, 193.
45. (a) Becke, A. D. J Chem Phys 1993, 98, 5648
46. (b) Lee, C.; Yang, W.; Parr, R. G. Phys Rev B 1988, 37, 785.
47. Dunning, T. H., Jr. J Chem Phys 1989, 90 1007.
48. Smimov, P. R.; Trostin, V. N. Russ. J Gen Chem 2007, 77, 844; and references therein.