-
1
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock, S.A. and McCammon, J.A. Molecular dynamics: Survey of methods for simulating the activity of proteins. Chemical Review, 106:1589-1615, 2006.
-
(2006)
Chemical Review
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
2
-
-
51049100635
-
Overcoming scaling challenges in biomolecular simulations across multiple platforms
-
to appear in, Miami, FL
-
Bhatele, A., Kumar, S., Mei, C., Phillips, J.C., Zheng, G., and Kale, L.V. Overcoming scaling challenges in biomolecular simulations across multiple platforms, to appear in Proceedings of the IEEE International Parallel and Distributed Processing Symposium (IPDPS 2008), Miami, FL, 2008.
-
(2008)
Proceedings of the IEEE International Parallel and Distributed Processing Symposium (IPDPS 2008)
-
-
Bhatele, A.1
Kumar, S.2
Mei, C.3
Phillips, J.C.4
Zheng, G.5
Kale, L.V.6
-
3
-
-
34548283148
-
Scalable algorithms for molecular dynamics simulations on commodity clusters
-
Tampa, FL
-
Bowers, K.J., Chow, E., xu, H., Dror, R.O., Eastwood, M.P., Gregersen, B.A., Klepeis, J.L., Kolossvary, I., Moraes, M.A., Sacerdoti, F.D., Salmon, J.K., Shan, Y., and Shaw, D.E. Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the ACM//IEEE Conference on Supercomputing (SC06), Tampa, FL, 2006.
-
(2006)
Proceedings of the ACM//IEEE Conference on Supercomputing (SC06)
-
-
Bowers, K.J.1
Chow, E.2
xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
Klepeis, J.L.7
Kolossvary, I.8
Moraes, M.A.9
Sacerdoti, F.D.10
Salmon, J.K.11
Shan, Y.12
Shaw, D.E.13
-
4
-
-
33846148305
-
Zonal methods for the parallel execution of range-limited N-body problems
-
Bowers, K.J., Dror, R.O., and Shaw, D.E. Zonal methods for the parallel execution of range-limited N-body problems. Journal of Computational Physics, 221(1):303-329, 2007.
-
(2007)
Journal of Computational Physics
, vol.221
, Issue.1
, pp. 303-329
-
-
Bowers, K.J.1
Dror, R.O.2
Shaw, D.E.3
-
5
-
-
40749094837
-
Blue matter: Scaling of N-body simulations to one atom per node
-
Fitch, B.G., Rayshubskiy, A., Eleftheriou, M., Ward, T.J.C., Giampapa, M.E., Pitman, M.C., Pitera, J.W., Swope, W.C., and Germain, R.S. Blue matter: scaling of N-body simulations to one atom per node. IBM Journal of Research and Development, 52(1/2), 2008.
-
(2008)
IBM Journal of Research and Development
, vol.52
, Issue.1-2
-
-
Fitch, B.G.1
Rayshubskiy, A.2
Eleftheriou, M.3
Ward, T.J.C.4
Giampapa, M.E.5
Pitman, M.C.6
Pitera, J.W.7
Swope, W.C.8
Germain, R.S.9
-
6
-
-
0026342528
-
-
Fine, R.D., Dimmler, G., and Levinthal, C. FASTRUN: A special purpose, hardwired computer for molecular simulation. Proteins: Structure, Function, and Genetics, 11(4):242-253, 1991 (erratum: 14(3):421-422, 1992).
-
Fine, R.D., Dimmler, G., and Levinthal, C. FASTRUN: A special purpose, hardwired computer for molecular simulation. Proteins: Structure, Function, and Genetics, 11(4):242-253, 1991 (erratum: 14(3):421-422, 1992).
-
-
-
-
7
-
-
27644594123
-
Blue matter on blue gene/L: Massively parallel computation for biomolecular simulation
-
New York, NY
-
Germain, R.S., Fitch, B., Rayshubskiy, A., Eleftheriou, M., Pitman, M.C., Suits, F., Giampapa, M., and Ward, T.J.C. Blue matter on blue gene/L: Massively parallel computation for biomolecular simulation. Proceedings of the Third IEEE/ACM/ IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES + ISSS '05), New York, NY, 2005.
-
(2005)
Proceedings of the Third IEEE/ACM/ IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES + ISSS '05)
-
-
Germain, R.S.1
Fitch, B.2
Rayshubskiy, A.3
Eleftheriou, M.4
Pitman, M.C.5
Suits, F.6
Giampapa, M.7
Ward, T.J.C.8
-
8
-
-
46249092554
-
GROMACS 4: Algorithms for highly effcient, load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. GROMACS 4: Algorithms for highly effcient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(2):435-447, 2008.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, Issue.2
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
9
-
-
0029912748
-
Development and testing of the OPLS all-atom force feld on conformational energetics and properties of organic liquids
-
Jorgensen, W.L., Maxwell, D.S., and Tirado-Rives, J. Development and testing of the OPLS all-atom force feld on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45):11225-11236, 1996.
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
10
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
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.
-
(1999)
Journal of Computational Physics
, vol.151
, Issue.1
, pp. 283-312
-
-
Kalé, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
11
-
-
0002098417
-
The development/ application of a "Minimalist" organic/ biomolecular mechanic forcefeld using a combination of ab initio calculations and experimental data
-
van Gunsteren, W.F. and Weiner, P.K. eds, Dordrecht, Netherlands:ESCOM, pp
-
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 forcefeld 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.
-
(1997)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
, pp. 83-96
-
-
Kollman, P.A.1
Dixon, R.W.2
Cornell, W.D.3
Fox, T.4
Chipot, C.5
Pohorille, A.6
-
12
-
-
57749209655
-
Incorporating fexibility in Anton, a specialized machine for molecular dynamics simulation
-
Salt Lake City, UT
-
Kuskin, J.S., Young, C., Grossman, J.P., Batson, B., Deneroff, M.M., Dror, R.O., and Shaw, D.E. Incorporating fexibility 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.
-
(2008)
Proceedings of the 14th International Symposium on High-Performance Computer Architecture (HPCA-14)
-
-
Kuskin, J.S.1
Young, C.2
Grossman, J.P.3
Batson, B.4
Deneroff, M.M.5
Dror, R.O.6
Shaw, D.E.7
-
13
-
-
57749191489
-
High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation
-
Salt Lake City, UT
-
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.
-
(2008)
Proceedings of the 14th International Symposium on High-Performance Computer Architecture (HPCA-14)
-
-
Larson, R.H.1
Salmon, J.K.2
Dror, R.O.3
Deneroff, M.M.4
Young, C.5
Grossman, J.P.6
Shan, Y.7
Klepeis, J.L.8
Shaw, D.E.9
-
14
-
-
0026372584
-
Molecular dynamics simulations on distributed memory machines
-
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.
-
(1991)
Computer Physics Communications
, vol.67
, Issue.2
, pp. 261-267
-
-
Liem, S.Y.1
Brown, D.2
Clarke, J.H.R.3
-
15
-
-
0041784950
-
-
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., Wió;rkiewicz-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.
-
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., Wió;rkiewicz-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
-
-
0037235952
-
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
-
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. Biopolymers, 68(1):91-109, 2003.
-
(2003)
Biopolymers
, vol.68
, Issue.1
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.P.4
Khaliq, S.5
Larson, S.M.6
Rhee, Y.M.7
Shirts, M.R.8
Snow, C.D.9
Sorin, E.J.10
Zagrovic, B.11
-
17
-
-
0343042644
-
Transient dynamics simulations: Parallel algorithms for contact detection and smoothed particle hydrodynamics
-
Pittsburgh, PA
-
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.
-
(1996)
Proceedings of the ACM//IEEE Conference on Supercomputing (Supercomputing '96)
-
-
Plimpton, S.J.1
Attaway, S.2
Hendrickson, B.3
Swegle, J.4
Vaughan, C.5
Gardner, D.6
-
18
-
-
22944460220
-
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
-
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.
-
(2005)
Journal of Chemical Physics
, vol.122
, pp. 054101
-
-
Shan, Y.1
Klepeis, J.L.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
19
-
-
24144495573
-
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions
-
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.
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.13
, pp. 1318-1328
-
-
Shaw, D.E.1
-
20
-
-
35348886062
-
-
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., Kolossvá;ry, 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.
-
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., Kolossvá;ry, 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
-
-
1642632943
-
A Note on N-body computations with cutoffs
-
Snir, M. A Note on N-body computations with cutoffs. Theory of Computing Systems, 37:295-318, 2004.
-
(2004)
Theory of Computing Systems
, vol.37
, pp. 295-318
-
-
Snir, M.1
-
22
-
-
84877051133
-
Protein explorer: A petafops special-purpose computer system for molecular dynamics simulations
-
Phoenix, AZ
-
Taiji, M., Narumi, T., Ohno, Y., Futatsugi, N., Suenaga, A., Takada, N., and Konagaya, A., Protein explorer: A petafops special-purpose computer system for molecular dynamics simulations. Proceedings of the ACM/IEEE Conference on Supercomputing (SC03), Phoenix, AZ, 2003.
-
(2003)
Proceedings of the ACM/IEEE Conference on Supercomputing (SC03)
-
-
Taiji, M.1
Narumi, T.2
Ohno, Y.3
Futatsugi, N.4
Suenaga, A.5
Takada, N.6
Konagaya, A.7
-
23
-
-
0001700958
-
Development of MD engine: High-speed accelerator with parallel processor design for molecular dynamics simulations
-
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.
-
(1999)
Journal Computational Chemistry
, vol.20
, Issue.2
, pp. 185-199
-
-
Toyoda, S.1
Miyagawa, H.2
Kitamura, K.3
Amisaki, T.4
Hashimoto, E.5
Ikeda, H.6
Kusumi, A.7
Miyakawa, N.8
-
24
-
-
34548524218
-
Fast evaluation of polarizableforces
-
Wang, W. and Skeel, R.D. Fast evaluation of polarizableforces. Journal of Chemical Physics, 123(16):164107, 2005.
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.16
, pp. 164107
-
-
Wang, W.1
Skeel, R.D.2
-
25
-
-
0035424713
-
Effcient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems
-
Zhou, R., Harder, E., xu, H., and Berne, B.J. Effcient 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.
-
(2001)
Journal of Chemical Physics
, vol.115
, Issue.5
, pp. 2348-2358
-
-
Zhou, R.1
Harder, E.2
xu, H.3
Berne, B.J.4
|