We investigate pairwise electrostatic interaction methods and show that there are viable computationally efficient alternatives to the Ewald summation for typical modern molecular simulations. These methods are extended from the damped and cutoff-neutralized Coulombic sum originally proposed by Wolf et al. [J. Chem. Phys. 110, 8255 (1999)]. One of these, the damped shifted force method, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. Comparisons were performed with this and other pairwise methods against the smooth particle-mesh Ewald summation to see how well they reproduce the energetics and dynamics of a variety of molecular simulations.
REFERENCES
1.
B.
Roux
and T.
Simonson
, Biophys. Chem.
78
, 1
(1999
).2.
C.
Sagui
and T. A.
Darden
, Annu. Rev. Biophys. Biomol. Struct.
28
, 155
(1999
).3.
D. J.
Tobias
, Curr. Opin. Struct. Biol.
11
, 253
(2001
).4.
5.
A.
Grossfield
, J.
Sachs
, and T. B.
Woolf
, Proteins
41
, 211
(2000
).6.
7.
P. J.
Steinbach
and B. R.
Brooks
, J. Comput. Chem.
15
, 667
(1994
).8.
L.
Onsager
, J. Am. Chem. Soc.
58
, 1486
(1936
).9.
V.
Rokhlin
, J. Comput. Phys.
60
, 187
(1985
).10.
D.
Wolf
, P.
Keblinski
, S. R.
Phillpot
, and J.
Eggebrecht
, J. Chem. Phys.
110
, 8255
(1999
).11.
12.
S. W.
de Leeuw
, J. W.
Perram
, and E. R.
Smith
, Proc. R. Soc. London, Ser. A
373
, 27
(1980
).13.
M. P.
Allen
and D. J.
Tildesley
, Computer Simulations of Liquids
(Oxford University Press
, New York
, 1987
).14.
S. G.
Brush
, H. L.
Sahlin
, and E.
Teller
, J. Chem. Phys.
45
, 2102
(1966
).15.
L. V.
Woodcock
and K.
Singer
, Trans. Faraday Soc.
67
, 12
(1971
).16.
17.
N.
Karasawa
and W. A.
Goddard
III, J. Phys. Chem.
93
, 7320
(1989
).18.
19.
J. W.
Perram
, H. G.
Petersen
, and S. W.
de Leeuw
, Mol. Phys.
65
, 875
(1988
).20.
R. W.
Hockney
and J. W.
Eastwood
, Computer Simulation Using Particles
(McGraw-Hill
, New York
, 1981
).21.
J.
Shimada
, H.
Kaneko
, and T.
Takada
, J. Comput. Chem.
14
, 867
(1993
).22.
B. A.
Luty
, M. E.
Davis
, I. G.
Tironi
, and W. F.
van Gunsteren
, Mol. Simul.
14
, 11
(1994
).23.
B. A.
Luty
, I. G.
Tironi
, and W. F.
van Gunsteren
, J. Chem. Phys.
103
, 3014
(1995
).24.
T.
Darden
, D.
York
, and L.
Pedersen
, J. Chem. Phys.
98
, 10089
(1993
).25.
U.
Essmann
, L.
Perera
, M. L.
Berkowitz
, T.
Darden
, H.
Lee
, and L. G.
Pedersen
, J. Chem. Phys.
103
, 8577
(1995
).26.
D. E.
Parry
, Surf. Sci.
49
, 433
(1975
).27.
D. E.
Parry
, Surf. Sci.
54
, 195
(1976
).28.
29.
30.
Y.-J.
Rhee
, J. W.
Halley
, J.
Hautman
, and A.
Rahman
, Phys. Rev. B
40
, 36
(1989
).31.
E.
Spohr
, J. Chem. Phys.
107
, 6342
(1997
).32.
I.-C.
Yeh
and M. L.
Berkowitz
, J. Chem. Phys.
111
, 3155
(1999
).33.
M.
Kawata
and M.
Mikami
, Chem. Phys. Lett.
340
, 157
(2001
).34.
A.
Arnold
, J.
de Joannis
, and C.
Holm
, J. Chem. Phys.
117
, 2496
(2002
).35.
J.
de Joannis
, A.
Arnold
, and C.
Holm
, J. Chem. Phys.
117
, 2503
(2002
).36.
37.
J. E.
Roberts
and J.
Schnitker
, J. Chem. Phys.
101
, 5024
(1994
).38.
J. E.
Roberts
and J.
Schnitker
, J. Phys. Chem.
99
, 1322
(1995
).39.
B. A.
Luty
and W. F.
van Gunsteren
, J. Phys. Chem.
100
, 2581
(1996
).40.
P. H.
Hünenberger
and J. A.
McCammon
, J. Chem. Phys.
110
, 1856
(1999
).41.
P. H.
Hünenberger
and J. A.
McCammon
, Biophys. Chem.
78
, 69
(1999
).42.
W.
Weber
, P. H.
Hünenberger
, and J. A.
McCammon
, J. Phys. Chem. B
104
, 3668
(2000
).43.
D.
Zahn
, B.
Schilling
, and S. M.
Kast
, J. Phys. Chem. B
106
, 10725
(2002
).44.
R. E.
Jones
and D. H.
Templeton
, J. Chem. Phys.
25
, 1062
(1956
).45.
D. M.
Heyes
, J. Chem. Phys.
74
, 1924
(1981
).46.
A.
Rahman
and F. H.
Stillinger
, J. Chem. Phys.
55
, 3336
(1971
).47.
D. J.
Adams
, E. M.
Adams
, and G. J.
Hills
, Mol. Phys.
38
, 387
(1979
).48.
T. A.
Andrea
, W. C.
Swope
, and H. C.
Andersen
, J. Chem. Phys.
79
, 4576
(1983
).49.
J. A.
Barker
and R. O.
Watts
, Mol. Phys.
26
, 789
(1973
).50.
N.
Metropolis
, A. W.
Rosenbluth
, M. N.
Rosenbluth
, A. H.
Teller
, and E.
Teller
, J. Chem. Phys.
21
, 1087
(1953
).51.
See EPAPS Document No. E-JCPSA6-124-515622 for a comparative analyses of the pairwise cutoff method performance for each of the seven model systems studied. This document can be reached via a direct link in the online article’s HTML reference section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
52.
H. J. C.
Berendsen
, J. R.
Grigera
, and T. P.
Straatsma
, J. Phys. Chem.
91
, 6269
(1987
).53.
M. A.
Meineke
, C. F.
Vardeman
II, T.
Lin
, C. J.
Fennell
, and J. D.
Gezelter
, J. Comput. Chem.
26
, 252
(2005
).54.
J. W.
Ponder
and F. M.
Richards
, J. Comput. Chem.
8
, 1016
(1987
).55.
A. R.
Leach
, Molecular Modeling: Principles and Applications
, 2nd ed. (Pearson Educated Limited
, Harlow, England
, 2001
).56.
S. M.
Kast
, K. F.
Schmidt
, and B.
Schilling
, Chem. Phys. Lett.
367
, 398
(2003
).© 2006 American Institute of Physics.
2006
American Institute of Physics
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