Mass and step length optimization for the calculation of equilibrium properties by molecular dynamics simulation

作者: Régis Pomès , J.Andrew McCammon

DOI: 10.1016/0009-2614(90)85055-H

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摘要: Abstract The effectiveness of combining an assumed hydrogen mass 10 amu with large step lengths up to fs in molecular dynamics calculations equilibrium properties pure water is investigated. Results are evaluated respect simulations featuring H 1 and time 2 fs. Although the increased reduces rate sampling configurations somewhat, this method allows a significant reduction computer needed calculate structural thermodynamic properties.

参考文章(12)
William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein, Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics. ,vol. 79, pp. 926- 935 ,(1983) , 10.1063/1.445869
Charles H. Bennett, Mass tensor molecular dynamics Journal of Computational Physics. ,vol. 19, pp. 267- 279 ,(1975) , 10.1016/0021-9991(75)90077-7
J. McCammon, Computer-aided molecular design. Science. ,vol. 238, pp. 486- 491 ,(1987) , 10.1126/SCIENCE.3310236
J.R. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Dinola, A., Haak, Molecular dynamics with coupling to an external bath Journal of Chemical Physics. ,vol. 81, pp. 3684- 3690 ,(1984) , 10.1063/1.448118
William L. Jorgensen, Free energy calculations: a breakthrough for modeling organic chemistry in solution Accounts of Chemical Research. ,vol. 22, pp. 184- 189 ,(1989) , 10.1021/AR00161A004
Bhalachandra L. Tembre, J.Andrew Mc Cammon, Ligand-receptor interactions Computational Biology and Chemistry. ,vol. 8, pp. 281- 283 ,(1984) , 10.1016/0097-8485(84)85020-2
Charles L. Brooks, B. Montgomery Pettitt, Martin Karplus, Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids Journal of Chemical Physics. ,vol. 83, pp. 5897- 5908 ,(1985) , 10.1063/1.449621
Johan P. M. Postma, Herman J. C. Berendsen, Jan R. Haak, Thermodynamics of cavity formation in water. A molecular dynamics study Faraday Symposia of The Chemical Society. ,vol. 17, pp. 55- 67 ,(1982) , 10.1039/FS9821700055
Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J.C Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes Journal of Computational Physics. ,vol. 23, pp. 327- 341 ,(1977) , 10.1016/0021-9991(77)90098-5
W. F. van Gunsteren, H. J. C. Berendsen, Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry Journal of Computer-Aided Molecular Design. ,vol. 1, pp. 171- 176 ,(1987) , 10.1007/BF01676960