We present a detailed analysis of the performance of the semiempirical divide and conquer method as compared with standard semiempirical MO calculations. The influence of different subsetting schemes involving dual buffer regions on the magnitude of the errors in energies and computational cost of the calculations are discussed. In addition, the results of geometry optimizations on several protein systems (453 to 4088 atoms) driven by a quasi-Newton algorithm are also presented. These results indicate that the divide and conquer approach gives reliable energies and gradients and suggest that protein geometry optimization using semiempirical methods can be routinely feasible using current computational resources.
REFERENCES
1.
2.
3.
4.
A. van der Vaart, V. Gogonea, S. L. Dixon, and K. M. Merz, Jr., J. Comput. Chem. (in press).
5.
X.-P.
Li
, R. W.
Nunes
, and D.
Vanderbilt
, Phys. Rev. B
47
, 10891
(1993
).6.
7.
A. D.
Daniels
, J. M.
Millam
, and G. E.
Scuseria
, J. Chem. Phys.
107
, 425
(1997
).8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
J. J.
Vincent
, S. L.
Dixon
, and K. M.
Merz
, Jr., Theor. Chem. Acc.
99
, 220
(1998
).18.
19.
20.
M. D.
Ermolaeva
, A.
van der Vaart
, and K. M. J.
Merz
, J. Phys. Chem.
103
, 1868
(1999
).21.
A.
van der Vaart
and K. M.
Merz
, Jr., J. Phys. Chem. A
103
, 3321
(1999
).22.
V.
Gogonea
, L. M.
Westerhoff
, and K. M.
Merz
, Jr., J. Chem. Phys.
113
, 1
(2000
).23.
A. D.
Daniels
, G. E.
Scuseria
, O.
Farkas
, and H. B.
Schlegel
, Int. J. Quantum Chem.
77
, 82
(2000
).24.
S. L. Dixon, A. van der Vaart, V. Gogonea, J. J. Vincent, E. N. Brothers, D. Suárez, L. M. Westerhoff, and K. M. Merz, Jr., DIVLON 99, The Pennsylvania State University, 1999.
25.
26.
27.
W. L.
Jorgensen
, J.
Chandrasekhar
, J.
Madura
, R. W.
Impey
, and M. L.
Klein
, J. Chem. Phys.
79
, 926
(1983
).28.
G.
Nadig
, L. C.
van Zant
, S. L.
Dixon
, and K. M.
Merz
, Jr., J. Am. Chem. Soc.
120
, 5593
(1998
).29.
M. J. S.
Dewar
, E. G.
Zoebisch
, E. F.
Healy
, and J. J. P.
Stewart
, J. Am. Chem. Soc.
107
, 3902
(1985
).30.
31.
32.
C.
Baysal
, H.
Meirovitch
, and I. M.
Navon
, J. Comput. Chem.
20
, 354
(1999
).33.
E. N. Brothers and K. M. Merz, Jr. (unpublished).
34.
C. Schafmeister, W. S. Ross, and V. Romanovski, LEAP 10 (University of California, San Francisco, 1995).
35.
D. A. Case, D. A. Pearlman, J. W. Caldwell et al., AMBER 5.0 ed. (University of California, San Francisco, 1997).
36.
W. D.
Cornell
, P.
Cieplak
, C. I.
Bayly
et al., J. Am. Chem. Soc.
117
, 5179
(1995
).37.
A. Cheng, R. S. Stanton, J. J. Vincent et al., ROAR 2.0 ed., The Pennsylvania State University, 1999.
38.
D. M.
York
, T.-S.
Lee
, and W.
Yang
, Phys. Rev. Lett.
80
, 5011
(1998
).39.
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
40.
41.
M. M.
Teeter
, S. M.
Roe
, and N. H.
Heo
, J. Mol. Biol.
230
, 292
(1993
).42.
C.
Van Alsenoy
, Y.
Ching-Hsing
, A.
Peeters
, J. M. L.
Martin
, and L.
Schäfer
, J. Phys. Chem. A
102
, 2245
(1998
).43.
G. J.
Hoover
, N.
Menhart
, A.
Martin
, S.
Warder
, and F. J.
Castellino
, Biochemistry
32
, 10936
(1993
).44.
45.
46.
M. C.
Vaney
, S.
Maignan
, M.
Ries-Kautt
, and A.
Ducruix
, Acta Crystallogr., Sect. D: Biol. Crystallogr.
52
, 505
(1996
).47.
D. E.
Kuehner
, J.
Engmann
, F.
Fergg
, M.
Wernick
, H. W.
Blanch
, and J. M.
Prausnitz
, J. Phys. Chem. B
103
, 1368
(1999
).
This content is only available via PDF.
© 2000 American Institute of Physics.
2000
American Institute of Physics
You do not currently have access to this content.
