Algorithms for parallel unconstrained minimization of molecular systems are examined. The overall framework of minimization is the same except for the choice of directions for updating the quasi-Newton Hessian. Ideally these directions are chosen so the updated Hessian gives steps that are same as using the Newton method. Three approaches to determine the directions for updating are presented: the straightforward approach of simply cycling through the Cartesian unit vectors (finite difference), a concurrent set of minimizations, and the Lanczos method. We show the importance of using preconditioning and a multiple secant update in these approaches. For the Lanczos algorithm, an initial set of directions is required to start the method, and a number of possibilities are explored. To test the methods we used the standard 50-dimensional analytic Rosenbrock function. Results are also reported for the histidine dipeptide, the isoleucine tripeptide, and cyclic adenosine monophosphate. All of these systems show a significant speed-up with the number of processors up to about eight processors.

1.
C. L.
Janssen
and
I. M. B.
Nielsen
,
Parallel Computing in Quantum Chemistry
(
Taylor & Francis
,
Boca Raton, FL
,
2008
).
2.
J.
Baker
,
L.
Fusti-Molnar
, and
P.
Pulay
,
J. Phys. Chem. A
108
,
3040
(
2004
).
3.
P.
Brown
,
C.
Woods
,
S.
McIntosh-Smith
, and
F. R.
Manby
,
J. Chem. Theory Comput.
4
,
1620
(
2008
).
4.
T.
Furlani
,
J.
Kong
, and
P.
Gill
,
Comput. Phys. Commun.
128
,
170
(
2000
).
5.
C.
Gan
,
C.
Tymczak
, and
M.
Challacombe
,
J. Chem. Phys.
121
,
6608
(
2004
).
6.
J.
Baker
and
P.
Pulay
,
J. Comput. Chem.
23
,
1150
(
2002
).
7.
J.
Baker
and
M.
Shirel
,
Parallel Comput.
26
,
1011
(
2000
).
8.
M. W.
Feyereisen
,
R. A.
Kendall
,
J.
Nichols
,
D.
Dame
, and
J. T.
Golab
,
J. Comput. Chem.
14
,
818
(
1993
).
9.
J.
Kästner
,
J. M.
Carr
,
T. W.
Keal
,
W.
Thiel
,
A.
Wander
, and
P.
Sherwood
,
J. Phys. Chem. A
113
,
11856
(
2009
).
10.
B.
Peters
,
A.
Heyden
, and
A. T.
Bell
,
J. Chem. Phys.
120
,
7877
(
2004
).
11.
W. N.
E
,
W. Q.
Ren
, and
E.
Vanden-Eijnden
,
Phys. Rev. B
66
,
052301
(
2002
).
12.
S. K.
Burger
and
W. T.
Yang
,
J. Chem. Phys.
124
,
054109
(
2006
).
13.
G.
Henkelman
and
H.
Jonsson
,
J. Chem. Phys.
113
,
9978
(
2000
).
14.
J.
Nocedal
and
S.
Wright
,
Numerical Optimization
(
Springer
,
New York
,
1999
).
15.
R.
Fletcher
,
Practical Methods of Optimization
(
Wiley-Interscience
,
NY
,
1987
).
16.
S.
Nash
and
A.
Sofer
,
Math. Program.
45
,
529
(
1989
).
17.
R.
Schnabel
,
Parallel Comput.
21
,
875
(
1995
).
18.
R.
Byrd
,
R.
Schnabel
, and
G.
Shultz
,
Math. Program.
42
,
273
(
1988
).
19.
R.
Schnabel
, “
Quasi-Newton methods using multiple secant equations
,” Department of Computer Science, University of Colorado at Boulder Technical Report No. CU-CS-247-83,
1983
.
20.
G.
Golub
and
C.
Van Loan
,
Matrix Computations
(
The Johns Hopkins University Press
,
Baltimore, MD
,
1996
).
21.
L.
Liberti
and
N.
Maculan
,
Global Optimization: From Theory to Implementation
(
Springer
,
New York
,
2009
).
22.
S. L.
Ho
,
S.
Yang
,
G.
Ni
,
E. W. C.
Lo
, and
H. C.
Wong
,
IEEE Trans. Magn.
41
,
1756
(
2005
).
23.
J.
Baker
and
W.
Hehre
,
J. Comput. Chem.
12
,
606
(
1991
).
24.
J.
Baker
,
J. Comput. Chem.
14
,
1085
(
1993
).
25.
G.
Fogarasi
,
X.
Zhou
,
P. W.
Taylor
, and
P.
Pulay
,
J. Am. Chem. Soc.
114
,
8191
(
1992
).
26.
C.
Peng
,
P. Y.
Ayala
,
H. B.
Schlegel
, and
M. J.
Frisch
,
J. Comput. Chem.
17
,
49
(
1996
).
27.
V.
Bakken
and
T.
Helgaker
,
J. Chem. Phys.
117
,
9160
(
2002
).
28.
D.
Xie
and
T.
Schlick
,
SIAM J. Optim.
10
,
132
(
1999
).
29.
E.
Koslover
and
D. J.
Wales
,
J. Chem. Phys.
127
,
234105
(
2007
).
30.
A.
Ghysels
,
D.
Van Neck
,
V.
Van Speybroeck
,
T.
Verstraelen
, and
M.
Warquier
,
J. Chem. Phys.
126
,
224102
(
2007
).
31.
A.
Ghysels
,
D.
Van Neck
, and
M.
Waroquier
,
J. Chem. Phys.
127
,
164108
(
2007
).
32.
A.
Ghysels
,
D.
Van Neck
,
B. R.
Brooks
,
V.
Van Speybroeck
, and
M.
Waroquier
,
J. Chem. Phys.
130
,
084107
(
2009
).
33.
D.
Kincaid
and
W.
Cheney
,
Numerical Analysis
(
Brooks/Cole
,
Belmont, CA
,
1991
).
34.
S. K.
Burger
,
L.
Yui
, and
P. W.
Ayers
, FORTRAN 90 code available at http://www.chemistry.mcmaster.ca/ayers/projects.html.
35.
M. J.
Frisch
,
H. B.
Schlegel
,
G. E.
Scuseria
,
M. A.
Robb
,
J. R.
Cheeseman
,
J. A.
Montgomery
, Jr.
,
T.
Vreven
,
K. N.
Kudin
,
J. C.
Burant
,
J. M.
Millam
,
S. S.
Iyengar
,
J.
Tomasi
,
V.
Barone
,
B.
Mennucci
,
M.
Cossi
,
G.
Scalmani
,
N.
Rega
,
G. A.
Petersson
,
H.
Nakatsuji
,
M.
Hada
,
M.
Ehara
,
K.
Toyota
,
R.
Fukuda
,
J.
Hasegawa
,
M.
Ishida
,
T.
Nakajima
,
Y.
Honda
,
O.
Kitao
,
H.
Nakai
,
M.
Klene
,
X.
Li
,
J. E.
Knox
,
H. P.
Hratchian
,
J. B.
Cross
,
V.
Bakken
,
C.
Adamo
,
J.
Jaramillo
,
R.
Gomperts
,
R. E.
Stratmann
,
O.
Yazyev
,
A. J.
Austin
,
R.
Cammi
,
C.
Pomelli
,
J. W.
Ochterski
,
P. Y.
Ayala
,
K.
Morokuma
,
G. A.
Voth
,
P.
Salvador
,
J. J.
Dannenberg
,
V. G.
Zakrzewski
,
S.
Dapprich
,
A. D.
Daniels
,
M. C.
Strain
,
O.
Farkas
,
D. K.
Malick
,
A. D.
Rabuck
,
K.
Raghavachari
,
J. B.
Foresman
,
J. V.
Ortiz
,
Q.
Cui
,
A. G.
Baboul
,
S.
Clifford
,
J.
Cioslowski
,
B. B.
Stefanov
,
G.
Liu
,
A.
Liashenko
,
P.
Piskorz
,
I.
Komaromi
,
R. L.
Martin
,
D. J.
Fox
,
T.
Keith
,
M. A.
Al-Laham
,
C. Y.
Peng
,
A.
Nanayakkara
,
M.
Challacombe
,
P. M. W.
Gill
,
B.
Johnson
,
W.
Chen
,
M. W.
Wong
,
C.
Gonzalez
, and
J. A.
Pople
, GAUSSIAN03, Revision C.02, Gaussian Inc., Wallingford, CT,
2004
.
36.
GAUSSVIEW, version 3.0, Gaussian, Inc., Pittsburgh, PA,
2003
.
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