-
1
-
-
33646943202
-
Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
-
S. A. Adcock and J. A. McCammon, Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins, Chem. Rev., 106: 1589-1615, 2006.
-
(2006)
Chem. Rev
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
2
-
-
34548283148
-
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
-
Tampa, FL
-
K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw, Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, in Proc. ACM/IEEE Conf. on Supercomputing (SC06), Tampa, FL, 2006.
-
(2006)
Proc. ACM/IEEE Conf. 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
-
3
-
-
34548287567
-
Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics
-
Tampa, FL
-
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. E. Giampapa, M. C. Pitman, and R. S. Germain, Blue Matter: Approaching the Limits of Concurrency for Classical Molecular Dynamics, in Proc. ACM/IEEE Conf. on Supercomputing (SC06), Tampa, FL, 2006.
-
(2006)
Proc. ACM/IEEE Conf. on Supercomputing (SC06)
-
-
Fitch, B.G.1
Rayshubskiy, A.2
Eleftheriou, M.3
Ward, T.J.C.4
Giampapa, M.E.5
Pitman, M.C.6
Germain, R.S.7
-
4
-
-
33746603053
-
-
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. E. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, S. Feller, and R. S. Germain, Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, in Proc. International Conf. on Computational Science (ICCS 2006), V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, Eds., Springer-Verlag, LNCS, 3992: 846-854, 2006.
-
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. E. Giampapa, Y. Zhestkov, M. C. Pitman, F. Suits, A. Grossfield, J. Pitera, W. Swope, R. Zhou, S. Feller, and R. S. Germain, Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, in Proc. International Conf. on Computational Science (ICCS 2006), V. Alexandrov, D. van Albada, P. Sloot, and J. Dongarra, Eds., Springer-Verlag, LNCS, 3992: 846-854, 2006.
-
-
-
-
6
-
-
27644594123
-
Blue Matter on Blue Gene/L: Massively Parallel Computation for Biomolecular Simulation
-
New York, NY
-
R. S. Germain, B. Fitch, A. Rayshubskiy, M. Eleftheriou, M. C. Pitman, F. Suits, M. Giampapa, and T. J. C. Ward, Blue Matter on Blue Gene/L: Massively Parallel Computation for Biomolecular Simulation, in Proc. 3rd IEEE/ACM/IFIP International Conf. on Hardware/Software Codesign and System Synthesis (CODES+ISSS '05), 207-212, New York, NY, 2005.
-
(2005)
Proc. 3rd IEEE/ACM/IFIP International Conf. on Hardware/Software Codesign and System Synthesis (CODES+ISSS '05)
, pp. 207-212
-
-
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
-
7
-
-
0029912748
-
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
-
W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc., 118(45): 11225-11236, 1996.
-
(1996)
J. Am. Chem. Soc
, vol.118
, Issue.45
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
8
-
-
0002098417
-
Minimalist Organic/ Biomolecular Mechanic Forcefield Using a Combination of Ab Initio Calculations and Experimental Data
-
The Development/Application of a, W. F. van Gunsteren and P. K. Weiner, Eds. Dordrecht, Netherlands: ESCOM
-
P. A. Kollman, R. W. Dixon, W. D. Cornell, T. Fox, C. Chipot, and A. Pohorille, 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, W. F. van Gunsteren and P. K. Weiner, Eds. Dordrecht, Netherlands: ESCOM, 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
-
9
-
-
0035871686
-
SHAKE Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations
-
V. Krautler, W. F. van Gunsteren, P. H. Hunenberger, A Fast SHAKE Algorithm to Solve Distance Constraint Equations for Small Molecules in Molecular Dynamics Simulations, J. Comput. Chem. 22 (5): 501-508, 2001.
-
(2001)
J. Comput. Chem
, vol.22
, Issue.5
, pp. 501-508
-
-
Krautler, V.1
van Gunsteren, W.F.2
Hunenberger, P.H.3
Fast, A.4
-
10
-
-
57749191489
-
High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation
-
Salt Lake City, UT
-
R. H. Larson, J. K. Salmon, R. O. Dror, M. M. Deneroff, C. Young, J.P. Grossman, J. L. Klepeis, and D. E. Shaw, High-Throughput Pairwise Point Interactions in Anton, a Specialized Machine for Molecular Dynamics Simulation, in Proc. 14th International Symposium on Computer Architecture (HPCA 2008), Salt Lake City, UT, 2008.
-
(2008)
Proc. 14th International Symposium on Computer Architecture (HPCA 2008)
-
-
Larson, R.H.1
Salmon, J.K.2
Dror, R.O.3
Deneroff, M.M.4
Young, C.5
Grossman, J.P.6
Klepeis, J.L.7
Shaw, D.E.8
-
11
-
-
0041784950
-
-
J. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. J. Karplus, All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B, 102(18): 3586-3616, 1998.
-
J. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. J. Karplus, All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins, J. Phys. Chem. B, 102(18): 3586-3616, 1998.
-
-
-
-
12
-
-
57749187695
-
-
MD Benchmarks for Amber, CHARMM and NAMD, See
-
MD Benchmarks for Amber, CHARMM and NAMD, See http://amber.scripps.edu/ amber8.bench2.html.
-
-
-
-
13
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, and K. Schulten, Scalable Molecular Dynamics with NAMD, J. Comput. Chem., 26(16): 1781-1802, 2005.
-
(2005)
J. Comput. Chem
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
14
-
-
85190297390
-
-
T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, Algorithmic Challenges in Computational Molecular Biophysics, J. Comput. Phys., 151(1): 9-48, 1999.
-
T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, Algorithmic Challenges in Computational Molecular Biophysics, J. Comput. Phys., 151(1): 9-48, 1999.
-
-
-
-
15
-
-
22944460220
-
Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation
-
Y. Shan, J. L. Klepeis, M. P. Eastwood, R. O. Dror, and D. E. Shaw, Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation, J. Chem. Phys., 122:054101, 2005.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 054101
-
-
Shan, Y.1
Klepeis, J.L.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
16
-
-
35348886062
-
-
D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J.P. Grossman, C. R. Ho, D. J. Ierardi, I. Kolossváry, J. L. Klepeis, T. Layman, C. McLeavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, S. C. Wang, Anton: A Special-Purpose Machine for Molecular Dynamics Simulation, in Proc. 34th International Symposium on Computer Architecture (ISCA'07), 1-12, San Diego, CA, 2007.
-
D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson, J. K. Salmon, C. Young, B. Batson, K. J. Bowers, J. C. Chao, M. P. Eastwood, J. Gagliardo, J.P. Grossman, C. R. Ho, D. J. Ierardi, I. Kolossváry, J. L. Klepeis, T. Layman, C. McLeavey, M. A. Moraes, R. Mueller, E. C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, S. C. Wang, Anton: A Special-Purpose Machine for Molecular Dynamics Simulation, in Proc. 34th International Symposium on Computer Architecture (ISCA'07), 1-12, San Diego, CA, 2007.
-
-
-
-
17
-
-
20744446407
-
On Computing The Fast Fourier Transform
-
R. C. Singleton, On Computing The Fast Fourier Transform, Commun. ACM, 10(10): 647-654, 1967.
-
(1967)
Commun. ACM
, vol.10
, Issue.10
, pp. 647-654
-
-
Singleton, R.C.1
-
18
-
-
84877051133
-
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations
-
Phoenix, AZ
-
M. Taiji, T. Narumi, Y. Ohno, N. Futatsugi, A. Suenaga, N. Takada, A. Konagaya, Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations, in Proc. ACM/IEEE Conf. on Supercomputing (SC03), Phoenix, AZ, 2003.
-
(2003)
Proc. ACM/IEEE Conf. on Supercomputing (SC03)
-
-
Taiji, M.1
Narumi, T.2
Ohno, Y.3
Futatsugi, N.4
Suenaga, A.5
Takada, N.6
Konagaya, A.7
-
19
-
-
57749173919
-
-
Tensilica, Inc, See http
-
Tensilica, Inc., Xtensa LX Product Brief. See http://www. tensilica.com.
-
Xtensa LX Product Brief
-
-
-
20
-
-
27344454932
-
Fast, Flexible, and Free
-
GROMACS
-
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, GROMACS: Fast, Flexible, and Free, J. Comput. Chem., 26(16): 1701-1718, 2005.
-
(2005)
J. Comput. Chem
, vol.26
, Issue.16
, pp. 1701-1718
-
-
van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
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