Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study

Biophysical Chemistry

Volumn 78, Issue 1-2, 1999, Pages 69-88

  Hunenberger P H ^a   McCammon, J A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Conformational equilibria; Continuum electrostatics; Ewald summation; Periodic boundary conditions

Indexed keywords

OLIGODEOXYNUCLEOTIDE; OLIGOPEPTIDE; POLYALANINE; PROTEIN; UNCLASSIFIED DRUG;

ARTIFACT; COMPUTER SIMULATION; CONFERENCE PAPER; ELECTRICITY; MOLECULAR DYNAMICS; PERIODICITY; PRIORITY JOURNAL; PROTEIN FOLDING; SOLVATION; TECHNIQUE; THEORY;

ALGORITHMS; BACTERIAL PROTEINS; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; OLIGOPEPTIDES; POLYAMINES; PROTEIN CONFORMATION; SOLVENTS;

EID: 0037627173     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(99)00007-1     Document Type: Conference Paper

References (78)

1. Harvey S.C. Proteins: Struct. Funct. Genet. 5:1989;78.
2. Davis M.E., McCammon J.A. Chem. Rev. 90:1990;509.
3. H.J.C. Berendsen, in: W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson (Eds.), Electrostatic Interactions (Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, vol. II, ESCOM, Leiden, 1993, p. 161.
4. P.E. Smith, W.F. van Gunsteren, in: W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson (Eds.), Methods for the Evaluation of Long Range Electrostatic Forces in Computer Simulations of Molecular Systems (Computer simulation of biomolecular systems, theoretical and experimental applications, vol. II, ESCOM, Leiden, 1993, p. 182.
5. Levy R.M., Gallicchio E. Annu. Rev. Phys. Chem. 49:1998;531.
6. M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids, Oxford University Press, New York, 1987.
7. de Leeuw S.W., Perram J.W., Smith E.R. Proc. R. Soc. London, Ser A. 373:1980;27.
8. Toukmaji A.Y., Board J.A. Jr. Comput. Phys. Commun. 95:1996;73.
9. R.W. Hockney, J.W. Eastwood, Computer Simulation using Particles, Institute of Physics Publishing, Bristol, 1988.
10. Luty B.A., Davis M.E., Tironi I.G., van Gunsteren W.F. Mol. Sim. 14:1994;11.
11. Luty B.A., Tironi I.G., van Gunsteren W.F. J. Chem. Phys. 103:1995;3014.
12. Darden T., York D., Pedersen L. J. Chem. Phys. 98:1993;10089.
13. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. J. Chem. Phys. 103:1995;8577.
14. Petersen H.G. J. Chem. Phys. 103:1995;3668.
15. White C.A., Head-Gordon M. J. Chem. Phys. 101:1994;6593.
16. Figueirido F., Levy R.M., Zhou R., Berne B.J. J. Phys. Chem. 106:1997;9835.
17. Challacombe M., White C., Head-Gordon M. J. Chem. Phys. 107:1997;10131.
18. Neumann M. Mol. Phys. 50:1983;841.
19. Neumann M., Steinhauser O., Pawley G.S. Mol. Phys. 52:1984;97.
20. Brooks III C.L. J. Chem. Phys. 86:1987;5156.
21. Madura J.D., Pettitt B.M. Chem. Phys. Lett. 150:1988;105.
22. Straatsma T.P., Berendsen H.J.C. J. Chem. Phys. 89:1989;5876.
23. Wood R.H. J. Chem. Phys. 103:1995;6177.
24. Pettitt B.M., Rossky P.J. J. Chem. Phys. 84:1986;5836.
25. Dang L.X., Pettitt B.M. J. Phys. Chem. 94:1990;4303.
26. Guàrdia E., Rey R., Padró J.A. J. Chem. Phys. 95:1991;2823.
27. Dang L.X., Pettitt B.M., Rossky P.J. J. Chem. Phys. 96:1992;4046.
28. Bader J.S., Chandler D. J. Phys. Chem. 96:1992;6423.
29. Hummer G., Soumpasis D.M., Neumann M. Mol. Phys. 81:1993;1155.
30. Del Buono G.S., Figueirido F.E., Levy R.M. Chem. Phys. Lett. 263:1996;521.
31. Smith P.E., Pettitt B.M. J. Chem. Phys. 95:1991;8430.
32. Schreiber H., Steinhauser O. Biochemistry. 31:1992;5856.
33. Schreiber H., Steinhauser O. Chem. Phys. 168:1992;75.
34. Schreiber H., Steinhauser O. J. Mol. Biol. 228:1992;909.
35. Loncharich R.J., Brooks B.R. Proteins: Struct. Funct. Genet. 6:1989;32.
36. Steinbach P.J., Brooks B.R. J. Comput. Chem. 15:1994;667.
37. Barker J.A., Watts R.O. Mol. Phys. 26:1973;789.
38. Alper H., Levy R.M. J. Chem. Phys. 91:1989;1242.
39. Hummer G., Soumpasis D.M. J. Phys.: Condens. Matter. 6:1994;A141.
40. Tironi I.G., Sperb R., Smith P.E., van Gunsteren W.F. J. Chem. Phys. 102:1995;5451.
41. Hünenberger P.H., van Gunsteren W.F. J. Chem. Phys. 108:1998;6117.
42. Del Buono G.S., Cohen T.S., Rossky P.J. J. Mol. Liq. 60:1994;221.
43. Lau K.F., Alper H.E., Thatcher T.S., Stouch T.E. J. Phys. Chem. 98:1994;8785.
44. Perera L., Essmann U., Berkowitz M.L. J. Chem. Phys. 102:1994;450.
45. York D.M., Darden T.A., Pedersen L.G. J. Chem. Phys. 99:1993;8345.
46. Fox T., Kollman P.A. Proteins: Struct. Funct. Genet. 25:1996;315.
47. Mohan V., Smith P.E., Pettitt B.M. J. Phys. Chem. 97:1993;12984.
48. Cheatham III T.E., Kollman P.A. J. Mol. Biol. 259:1996;434.
49. Cheatham III T.E., Kollman P.A. Structure. 5:1997;1297.
50. Cheatham III T.E., Crowley M.F., Fox T., Kollman T., Kollman P.A. Proc. Natl. Acad. Sci. USA. 94:1997;9626.
51. Young M.A., Ravishanker G., Beveridge D.L. Biophys. J. 73:1997;2313.
52. Auffinger P., Westhof E. J. Mol. Biol. 269:1996;326.
53. Auffinger P., Westhof E. Curr. Opin. Struct. Biol. 8:1998;227.
54. Smith P.E., Pettitt B.M. J. Chem. Phys. 105:1996;4289.
55. Hummer G., Pratt L.R., Garcia A.E. J. Phys. Chem. 100:1996;1206.
56. Figueirido F., Del Buono G.S., Levy R.M. J. Phys. Chem. B. 101:1997;5622.
57. Hummer G., Pratt L.R., Garcia A.E. J. Chem. Phys. 107:1997;9275.
58. Hünenberger P.H., McCammon J.A. J. Chem. Phys. 101:1999;1856.
59. Nijboer B.R.A., Ruijgrok T.W. J. Stat. Phys. 53:1988;361.
60. Cichocki B., Felderhof B.U., Hinsen K. Phys. Rev. A. 39:1989;5350.
61. Hummer G., Soumpasis D.M. J. Chem. Phys. 98:1993;581.
62. Figueirido F., Del Buono G.S., Levy R.M. J. Chem. Phys. 103:1995;6133.
63. Norberto de Souza O., Ornstein R.L. Biophys. J. 72:1997;2395.
64. Reddy T.R., Suryanarayana T. Biochem. Biophys. Acta. 949:1988;87.
65. McAfee J.G., Edmondson S.P., Datta P.K., Shriver J.W., Gupta R. Biochemistry. 34:1995;10063.
66. Edmondson S.P., Qiu L., Shriver J.W. Biochemistry. 34:1995;13289.
67. de Bakker P.I.W., Hünenberger P.H., McCammon J.A. J. Mol. Biol. 285:1999;1811.
68. J.D. Madura, M.E. Davis, M.K. Gilson, R.C. Wade, B.A. Luty, J.A. McCammon, in: K.B. Lipkowitz, D.B. Boyd (Eds.), Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations (Reviews in computational chemistry, vol. 4), VCH, New York, 1994, p. 229.
69. MOLECULAR SIMULATION INC., Quanta version 4.0 parameter handbook. 200 Fifth Avenue, Waltham, MA 02154 (1992).
70. Goodsell D.S., Grzeskowiak K., Dickerson R.E. Biochemistry. 34:1995;1022.
71. W.F. van Gunsteren, S.R. Billeter, A.A. Eising et al. Biomolecular Simulation: The GROMOS96 Manual and User Guide, Verlag der Fachvereine, Zürich, 1996.
72. Daggett V., Levitt M. J. Mol. Biol. 232:1993;600.
73. Tirado-Rives J., Jorgensen W.L. Biochemistry. 32:1993;4175.
74. Hünenberger P.H., Mark A.E., van Gunsteren W.F. Proteins: Struct. Funct. Genet. 21:1995;196.
75. Caflisch A., Karplus M. J. Mol. Biol. 252:1995;672.
76. Onsager L. J. Am. Chem. Soc. 58:1936;1486.
77. Born M. Z. Phys. 1:1920;45.
78. Luty B.A., van Gunsteren W.F. J. Phys. Chem. 100:1996;2581.