Journal of the American Chemical
Society, 118( 45):11225––11236, 1996.
10. Kalé, L., Skeel, R., Bhandarkar, M.,
Brunner, R., Gursoy, A., Krawetz,
N., Phillips, J., Shinozaki, A.,
Varadarajan, K., and Schulten,
K., NAMD2: Greater scalability
for parallel molecular dynamics.
Journal of Computational Physics,
151( 1):283––312, 1999.
11. Kollman, P.A., Dixon, R. W., Cornell,
W.D., Fox, T., Chipot, C., and
Pohorille, A. The development/
application of a “Minimalist” organic/
biomolecular mechanic forcefield
using a combination of ab initio
calculations and experimental
data, in Computer Simulation of
Biomolecular Systems: Theoretical
and Experimental Applications, van
Gunsteren, W.F. and Weiner, P.K. eds.,
Dordrecht, Netherlands:ESCOM, pp.
83–– 96, 1997.
12. Kuskin, J.S., Young, C., Grossman,
J.P., Batson, B., Deneroff, M.M., Dror,
R.O., and Shaw, D.E. Incorporating
flexibility in Anton, a specialized
machine for molecular dynamics
simulation. Proceedings of the 14th
International Symposium on High-Performance Computer Architecture
(HPCA- 14), Salt Lake City, UT, 2008.
13. Larson, R.H., Salmon, J.K., Dror, R.O.,
Deneroff, M.M., Young. C., Grossman,
J.P., Shan, Y., Klepeis, J.L., and Shaw,
D.E. High-throughput pairwise point
interactions in Anton, a specialized
machine for molecular dynamics
simulation. Proceedings of the
14th International Symposium
on High-Performance Computer
Architecture (HPCA- 14), Salt
Lake City, UT, 2008.
14. Liem, S. Y., Brown, D., and Clarke,
J.H.R. Molecular dynamics simulations
on distributed memory machines.
Computer Physics Communications,
67( 2):261––267, 1991.
15. MacKerell, A.D. Jr., Bashford, D.,
Bellott, M., Dunbrack, R.L., Evanseck,
J.D., Field, M.J., Fischer, S., Gao, J.,
Guo, H., Ha, S., Joseph-McCarthy, D.,
Kuchnir, L., Kuczera, K., Lau, F. T.K.,
Mattos, C., Michnick, S., Ngo, T.,
Nguyen, D. T., Prodhom, B., Reiher,
III, W.E. , Roux, B., Schlenkrich,
M., Smith, J. C., Stote, R., Straub, J.,
Watanabe, M., Wiórkiewicz-Kuczera,
J., Yin, D., and Karplus, M.J. All-atom
empirical potential for molecular
modeling and dynamics studies of
proteins. Journal of Physical Chemistry
B, 102( 18):3586––3616, 1998.
16. Pande, V.S., Baker, I., Chapman, J.,
Elmer, S.P., Khaliq, S., Larson, S.M.,
Rhee, Y.M., Shirts, M.R., Snow, C. D.,
Sorin, E.J., and Zagrovic, B. Atomistic
protein folding simulations on the
submillisecond time scale using
worldwide distributed computing.
David E. Shaw (David. Shaw@DEShaw
Research.com) Center for Computational
Biology and Bioinformatics, Columbia
University, New York, N Y 10032
© 2008 ACM 0001-0782/08/0700 $5.00
Biopolymers, 68( 1): 91–– 109, 2003.
17. Plimpton, S.J., Attaway, S.,
Hendrickson, B., Swegle, J., Vaughan,
C., and Gardner, D. Transient dynamics
simulations: Parallel algorithms for
contact detection and smoothed
particle hydrodynamics. Proceedings
of the ACM//IEEE Conference on
Supercomputing (Supercomputing
‘ 96), Pittsburgh, PA, 1996.
18. Shan, Y., Klepeis, J.L., Eastwood, M.P.,
Dror, R.O., and Shaw, D.E. Gaussian
split Ewald: A fast Ewald mesh
method for molecular simulation.
Journal of Chemical Physics,
122:054101, 2005.
19. Shaw, D.E. A fast, scalable
method for the parallel evaluation
of distance-limited pairwise
particle interactions. Journal
of Computational Chemistry,
26( 13):1318––1328, 2005.
20. Shaw, D.E., Deneroff, M.M., Dror, R.O.,
Kuskin, J.S., Larson, R.H., Salmon,
J.K., Young, C., Batson, B., Bowers,
K.J., Chao, J.C., Eastwood, M.P.,
Gagliardo, J., Grossman, J.P., Ho,
C.R., Ierardi, D.J., Kolossváry, I.,
Klepeis, J.L., Layman, T., McLeavey,
C., Moraes, M.A., Mueller, R.,
Priest, E.C., Shan, Y., Spengler, J.,
Theobald, M., Towles, B., and Wang,
S.C., Anton, a special purpose
machine for molecular dynamics
simulation. Proceedings of the 34th
Annual International Symposium
on Computer Architecture (ISCA
‘07), San Diego, CA, 2007.
21. Snir, M. A Note on N-body computations
with cutoffs. Theory of Computing
Systems, 37:295––318, 2004.
22. Taiji, M., Narumi, T., Ohno, Y.,
Futatsugi, N., Suenaga, A., Takada, N.,
and Konagaya, A., Protein explorer:
A petaflops special-purpose
computer system for molecular
dynamics simulations. Proceedings
of the ACM/IEEE Conference on
Supercomputing (SC03), Phoenix,
AZ, 2003.
23. Toyoda, S., Miyagawa, H., Kitamura,
K., Amisaki, T., Hashimoto,
E., Ikeda, H., Kusumi, A., and
Miyakawa, N. Development of MD
engine: High-speed accelerator
with parallel processor design for
molecular dynamics simulations.
Journal Computational Chemistry,
20( 2): 185––199, 1999.
24. Wang, W. and Skeel, R.D. Fast
evaluation of polarizableforces.
Journal of Chemical Physics,
123( 16):164107, 2005.
25. Zhou, R., Harder, E., xu, H., and
Berne, B.J. Efficient multiple time
step method for use with Ewald
and particle mesh Ewald for large
biomolecular systems. Journal of
Chemical Physics, 115( 5):
2348––2358, 2001.
ACM TRANSACTIONS ON
INTERNET TECHNOLOGY
Transactions on Internet Technology (TOIT). This quarterly publication encompasses many disciplines in computing—including computer software engineering, middleware,
database management, security, knowledge discovery and
data mining, networking and distributed systems, communications, and performance and scalability—all under one
roof. TOIT brings a sharper focus on the results and roles of
the individual disciplines and the relationship among them.
Extensive multi-disciplinary coverage is placed on the new
application technologies, social issues, and public policies
shaping Internet development. Subscribe Today!
PRODUCT INFORMATION
ISSN: 1533-5399
Order Code: (140)
Price: $41 ProfessionalMember
$36 Student Member
$170 Non-Member
$16 Air Service (for residents
outside North America only)
TO PLACE AN ORDER
Contact ACM Member Services
Phone: 1.800.342.6626 Email: acmhelp@acm.org
(U.S. and Canada) Mail: ACM Member Services
+ 1.212.626.0500 General Post Office
(Global)
P.O. Box 30777
Fax: + 1.212.944.1318
(Hours: 8:30am—4:30pm, Eastern Time) New York, NY
10087-0777 USA
www.acm.org/pubs/periodicals/toit