Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations

Journal of Computational Chemistry

Volumn 30, Issue 9, 2009, Pages 1490-1498

  Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Coulomb; Lookup table; Speed; Van der Waals

Indexed keywords

ATOMIC INTERACTIONS; ATOMISTIC SIMULATIONS; BIOMOLECULAR SYSTEM; CLASSICAL SIMULATION; COULOMB; DIRECT CALCULATION; DOUBLE PRECISION; EXPLICIT WATER; FINITE RESOLUTION; FORTRAN 95; FORTRAN CODES; INNER LOOPS; INTERACTION FORCES; LINEAR INTERPOLATION; LOOKUP TABLE; MAIN MEMORY; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SYSTEMS; SQUARE ROOTS; VAN DER WAALS;

FORTRAN (PROGRAMMING LANGUAGE); MOLECULAR DYNAMICS; SPEED; VAN DER WAALS FORCES;

TABLE LOOKUP;

PROTEIN; WATER;

ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION;

COMPUTER SIMULATION; MODELS, CHEMICAL; PROTEINS; SOFTWARE; WATER;

EID: 67650135820     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21169     Document Type: Article

References (34)

1. McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature 1977, 267, 585.
2. Freddolino, P. L.; Arkhipov, A. S.; Larson, S. B.; McPherson, A.; Schulten, K. Structure 2006, 14, 437.
3. Sanbonmatsu, K. Y.; Tung, C. S. J Struct Biol 2007, 157, 470.
4. Elofsson, A.; Nilsson, L. J Mol Biol 1993, 233, 766.
5. Sugita, Y.; Kitao, A.; Okamoto, Y. J Chem Phys 2000, 113, 6042.
6. Norberg, J.; Nilsson, L. J Phys Chem 1995, 99, 13056.
7. Carlsson, P.; Burendahl, S.; Nilsson, L. Biophys J 2006, 91, 3151.
8. Verlet, L. Phys Rev 1969, 159, 98.
9. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
10. Malevanets, A.; Kapral, R. J Chem Phys 2000, 112, 7260.
11. Doruker, P.; Atilgan, A. R.; Bahar, I. Proteins 2000, 40, 512.
12. Roux, B.; Simonson, T. Biophys Chem 1999, 78(1/2), 1.
13. Feig, M.; Brooks, I.; Charles L. Curr Opin Struct Biol 2004, 14, 217.
14. Chun, H. M.; Padilla, C. E.; Chin, D. N.; Watanabe, M.; Karlov, V. I.; Alper, H. E.; Soosaar, K.; Blair, K. B.; Becker, O. M.; Caves, L. S. D.; Nagle, R.; Haney, D. N.; Farmer, B. L. J Comput Chem 2000, 21, 159.
15. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
16. Tuckerman, M.; Berne, B. J.; Martyna, G. J. J Chem Phys 1992, 97, 1990.
17. Watanabe, M.; Karplus, M. J Phys Chem 1995, 99, 5680.
18. Zhang, G. H.; Schlick, T. J Chem Phys 1994, 101, 4995.
19. Güntert, P.; Wüthrich, K. Comput Phys Commun 2001, 138, 155.
20. Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, 2006.
21. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J Comput Chem 2005, 26, 1701.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
23. Brooks, B. R.; Brooks, C. L., III; MacKerell Juniorperiod, A. D.; Nilsson, L.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Fischer, S.; Gao, J.; Hodoscek, M.; Kuczera, K.; Lazaridis, T.; Ma, J.; Paci, E.; Pastor, R. W.; Petrella, R. J.; Post, C. B.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; York, D. M.; Karplus, M. J Comput Chem (in press).
24. Steinbach, P. J.; Brooks, B. R. J Comput Chem 1994, 15, 667.
25. Brooks, C. L.; Pettitt, B. M.; Karplus, M. J Chem Phys 1985, 83, 5897.
26. Nosé, S. J Chem Phys 1984, 81, 511.
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
28. Mark, P.; Nilsson, L. J Comput Chem 2002, 23, 1211.
29. Porat, A.; Lillig, C. H.; Johansson, C.; Fernandes, A. P.; Nilsson, L.; Holmgren, A.; Beckwith, J. Biochemistry 2007, 46, 3366.
30. MacKerell Juniorperiod, A. D.; Bashford, D.; Belott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
31. Feller, S. E.; Pastor, R. W.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. R. J Phys Chem 1996, 100, 17011.
32. Mark, P.; Nilsson, L. J Phys Chem A 2001, 105, 9954.
33. Höchtl, P.; Boresch, S.; Bitomsky, W.; Steinhauser, O. J Chem Phys 1998, 109, 4927.
34. Hess, B.; Kutzner, C.; vanderSpoel, D.; Lindahl, E. J Chem Theory Comput 2008, 4, 435.