-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
DOI 10.1038/nsb0902-646
-
Karplus M, McCammon JA. 2002 Molecular dynamics simulations of biomolecules. Nat. Struct. Mol. Biol. 9, 646-652. (doi:10.1038/nsb0902-646) (Pubitemid 34977295)
-
(2002)
Nature Structural Biology
, vol.9
, Issue.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
2
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case DA et al. 2005 The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688. (doi:10.1002/jcc.20290) (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
3
-
-
67650500988
-
CHARMM: The biomolecular simulation program
-
doi:10.1002/jcc.21287)
-
Brooks BR et al. 2009 CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545-1614. (doi:10.1002/jcc.21287)
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
-
4
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
DOI 10.1002/jcc.20289
-
Phillips JC et al. 2005 Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802. (doi:10.1002/jcc.20289) (Pubitemid 43078511)
-
(2005)
Journal of Computational Chemistry
, 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
Kale, L.9
Schulten, K.10
-
5
-
-
34548283148
-
Scalable algorithms for molecular dynamics simulations on commodity clusters
-
Tampa, FL November article no. New York, NY: ACM. (doi:10.1109/SC.2006. 54)
-
Bowers KJ et al. 2006 Scalable algorithms for molecular dynamics simulations on commodity clusters. In Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM), Tampa, FL, 11-17 November, article no. New York, NY: ACM. (doi:10.1109/SC.2006.54)
-
(2006)
Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM)
, pp. 11-17
-
-
Bowers, K.J.1
-
6
-
-
34548287567
-
Blue matter: Approaching the limits of concurrency for classical molecular dynamics
-
Tampa, FL November, article no. New York, NY: ACM. (doi:10.1109/SC.2006. 16)
-
Fitch BG, Rayshubskiy A, Eleftheriou M, Ward TC, Giampapa M, Pitman MC, Germain RS. 2006 Blue matter: Approaching the limits of concurrency for classical molecular dynamics. In Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM), Tampa, FL, 11-17 November, article no. New York, NY: ACM. (doi:10.1109/SC.2006.16)
-
(2006)
Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM)
, pp. 11-17
-
-
Fitch, B.G.1
Rayshubskiy, A.2
Eleftheriou, M.3
Ward, T.C.4
Giampapa, M.5
Pitman, M.C.6
Germain, R.S.7
-
7
-
-
64649105762
-
Accelerating molecular dynamic simulation on graphics processing units
-
doi:10.1002/jcc.21209)
-
Friedrichs MS et al. 2009 Accelerating molecular dynamic simulation on graphics processing units. J. Comput. Chem. 30, 864-872. (doi:10.1002/jcc.21209)
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 864-872
-
-
Friedrichs, M.S.1
-
8
-
-
24044541353
-
Design and implementation of the Delft molecular-dynamics processor
-
(ed. BJ Alder) San Diego, CA: Academic Press
-
Bakker AF, Bruin C. 1988 Design and implementation of the Delft molecular-dynamics processor. In Special purpose computers (ed. BJ Alder), pp. 183-232. San Diego, CA: Academic Press.
-
(1988)
Special Purpose Computers
, pp. 183-232
-
-
Bakker, A.F.1
Bruin, C.2
-
9
-
-
28144442197
-
A special purpose computer for molecular dynamics calculations
-
doi:10.1016/0021-9991 (9090169-909012)
-
Bakker AF, Gilmer GH, Grabow MH, Thompson K. 1990 A special purpose computer for molecular dynamics calculations. J. Comput. Phys. 90, 313-335. (doi:10.1016/0021-9991 (90)90169-2)
-
(1990)
J. Comput. Phys.
, vol.90
, pp. 313-335
-
-
Bakker, A.F.1
Gilmer, G.H.2
Grabow, M.H.3
Thompson, K.4
-
10
-
-
0026342528
-
FASTRUN: A special purpose, hardwired computer for molecular simulation
-
(doi:10.1002/prot.340 110403)
-
Fine R, Dimmler G, Levinthal C. 1991 FASTRUN: A special purpose, hardwired computer for molecular simulation. PROTEINS: Struct. Funct. Genet. 11, 242-253. (doi:10.1002/prot.340 110403)
-
(1991)
PROTEINS: Struct. Funct. Genet.
, vol.11
, pp. 242-253
-
-
Fine, R.1
Dimmler, G.2
Levinthal, C.3
-
11
-
-
0002741725
-
A special-purpose computer for gravitational many-body problems
-
Sugimoto D, Chikada Y, Makino J, Ito T, Ebisuzaki T, Umemura M. 1990 A specialpurpose computer for gravitational many-body problems. Nature 345, 33-35. (doi:10.1038/ 345033a0) (Pubitemid 120028804)
-
(1990)
Nature
, vol.345
, Issue.6270
, pp. 33-35
-
-
Sugimoto, D.1
Chikada, Y.2
Makino, J.3
Ito, T.4
Ebisuzaki, T.5
Umemura, M.6
-
12
-
-
0042889877
-
A special-purpose computer for gravitational many-body systems: GRAPE-2
-
Ito T, Makino J, Ebisuzaki T, Sugimoto D. 1991 A special-purpose computer for gravitational many-body systems: GRAPE-2. Publ. Astron. Soc. Japan 43, 547-555.
-
(1991)
Publ. Astron. Soc. Japan
, vol.43
, pp. 547-555
-
-
Ito, T.1
Makino, J.2
Ebisuzaki, T.3
Sugimoto, D.4
-
13
-
-
0040618693
-
GRAPE project: An overview
-
Ebisuzaki T, Makino J, Fukushige T, Taiji M, Sugimoto D, Ito T, Okumura SK. 1993 GRAPE project: An overview. Publ. Astron. Soc. Jpn 45, 269-278.
-
(1993)
Publ. Astron. Soc. Jpn
, vol.45
, pp. 269-278
-
-
Ebisuzaki, T.1
Makino, J.2
Fukushige, T.3
Taiji, M.4
Sugimoto, D.5
Ito, T.6
Okumura, S.K.7
-
14
-
-
0028092681
-
GRAPE-4: A teraFLOPS massively parallel special-purpose computer system for astrophysical N-body simulations
-
Cancun, Mexico, 26-29 April Piscataway, NJ: IEEE. (doi:10.1109/IPPS.1994. 288288)
-
Taiji M, Makino J, Ebisuzaki T, Sugimoto D. 1994 GRAPE-4: A teraFLOPS massively parallel special-purpose computer system for astrophysical N-body simulations. In Proc. Eighth International Parallel Processing Symp., Cancun, Mexico, 26-29 April, pp. 280-287. Piscataway, NJ: IEEE. (doi:10.1109/IPPS.1994. 288288)
-
(1994)
Proc. Eighth International Parallel Processing Symp
, pp. 280-287
-
-
Taiji, M.1
Makino, J.2
Ebisuzaki, T.3
Sugimoto, D.4
-
16
-
-
85105740186
-
1.34 Tflops molecular dynamics simulation for NaCl with a special-purpose computer: MDM
-
Dallas, TX, November. New York, NY: ACM. (doi:370049.370465)
-
Narumi T, Susukita R, Koishi T, Yasuoka K, Furusawa H, Kawai A, Ebisuzaki T. 2000 1.34 Tflops molecular dynamics simulation for NaCl with a special-purpose computer: MDM. In Proc. 2000 ACM/IEEE Conf. Supercomputing (CDROM), Dallas, TX, 4-10, November. New York, NY: ACM. (doi:370049.370465)
-
(2000)
Proc. 2000 ACM/IEEE Conf. Supercomputing (CDROM)
, pp. 4-10
-
-
Narumi, T.1
Susukita, R.2
Koishi, T.3
Yasuoka, K.4
Furusawa, H.5
Kawai, A.6
Ebisuzaki, T.7
-
17
-
-
84877051133
-
Protein explorer: A petaflops special-purpose computer system for molecular dynamics simulations
-
Phoenix, AZ 15-21 November. New York, NY: ACM doi:10.1145/1048935. 1050166)
-
Taiji M, Narumi T, Ohno Y, Futatsugi N, Suenaga A, Takada N, Konagaya A. 2003 Protein explorer: A petaflops special-purpose computer system for molecular dynamics simulations. In Proc. 2003 ACM/IEEE Conf. Supercomputing (CDROM), Phoenix, AZ, 15-21 November. New York, NY: ACM. (doi:10.1145/1048935.1050166)
-
(2003)
Proc. 2003 ACM/IEEE Conf. Supercomputing (CDROM)
-
-
Taiji, M.1
Narumi, T.2
Ohno, Y.3
Futatsugi, N.4
Suenaga, A.5
Takada, N.6
Konagaya, A.7
-
18
-
-
34548274117
-
A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3
-
Tampa, FL 11-17 November article no. New York, NY: ACM. (doi:10.1145/1188455.1188506)
-
Narumi T et al. 2006 A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3. In Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM), Tampa, FL, 11-17 November, article no. New York, NY: ACM. (doi:10.1145/1188455.1188506)
-
(2006)
Proc. 2006 ACM/IEEE Conf. Supercomputing (CDROM)
-
-
Narumi, T.1
-
19
-
-
35348886062
-
Anton, a special-purpose machine for molecular dynamics simulation
-
DOI 10.1145/1250662.1250664, ISCA'07: 34th Annual International Symposium on Computer Architecture, Conference Proceedings
-
Shaw DE et al. 2007 Anton, a special-purpose machine for molecular dynamics simulation. In Proc. 34th Annual Int. Symp. Computer Architecture. ISCA '07, San Diego, CA, 09-11 June, 2007, pp. 1-12. New York, NY: ACM. (doi:10.1145/1250662.1250664) (Pubitemid 47582086)
-
(2007)
Proceedings - International Symposium on Computer Architecture
, pp. 1-12
-
-
Shaw, D.E.1
Deneroff, M.M.2
Dror, R.O.3
Kuskin, J.S.4
Larson, R.H.5
Salmon, J.K.6
Young, C.7
Batson, B.8
Bowers, K.J.9
Chao, J.C.10
Eastwood, M.P.11
Gagliardo, J.12
Grossman, J.P.13
Ho, C.R.14
Ierardi, D.J.15
Kolossvary, I.16
Klepeis, J.L.17
Layman, T.18
McLeavey, C.19
Moraes, M.A.20
Mueller, R.21
Priest, E.C.22
Shan, Y.23
Spengler, J.24
Theobald, M.25
Towles, B.26
Wang, S.C.27
more..
-
20
-
-
74049112717
-
Millisecond-scale molecular dynamics simulations on Anton
-
Portland, OR 14-20 November article no. New York, NY: ACM. (doi:10.1145/1654059.1654099)
-
Shaw DE et al. 2009 Millisecond-scale molecular dynamics simulations on Anton. In Proc. 2009 ACM/IEEE Conf. Supercomputing (CDROM), Portland, OR, 14-20 November, article no. New York, NY: ACM. (doi:10.1145/1654059.1654099)
-
(2009)
Proc. 2009 ACM/IEEE Conf. Supercomputing (CDROM)
-
-
Shaw, D.E.1
-
21
-
-
84875592758
-
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
-
doi:10.1093/bioinformatics/btt055)
-
Pronk S et al. 2013 GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845-854. (doi:10.1093/bioinformatics/btt055)
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
-
22
-
-
33846823909
-
Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
-
doi:10.1063/1.464397)
-
Darden T, York D, Pedersen L. 1993 Particle mesh Ewald: An N log (N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10 089-10 092. (doi:10.1063/1.464397)
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
23
-
-
84977266737
-
Ewald summation
-
doi:10.1002/andp.19213690304)
-
Ewald PP. 1921 Ewald summation. Ann. Phys. 64, 253-371. (doi:10.1002/andp.19213690304)
-
(1921)
Ann. Phys.
, vol.64
, pp. 253-371
-
-
Ewald, P.P.1
-
24
-
-
33645961739
-
A smooth particle mesh Ewald method
-
doi:10.1063/1.470117)
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. 1995 A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593. (doi:10.1063/1.470117)
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
25
-
-
22944460220
-
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
-
doi:10.1063/1.1839571)
-
Shan Y, Klepeis JL, Eastwood MP, Dror RO, Shaw DE. 2005 Gaussian split Ewald: A fast Ewald mesh method for molecular simulation. J. Chem. Phys. 122, 54101. (doi:10.1063/1.1839571)
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 54101
-
-
Shan, Y.1
Klepeis, J.L.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
26
-
-
65649129896
-
MDGRAPE-3 chip: A 165 Gflops application specific LSI for molecular dynamics simulations
-
Taiji M. 2004 MDGRAPE-3 chip: A 165 Gflops application specific LSI for molecular dynamics simulations. Hot Chips 16, 198-202.
-
(2004)
Hot Chips
, vol.16
, pp. 198-202
-
-
Taiji, M.1
-
27
-
-
84929397261
-
-
Tensilica Inc, Santa Clara CA: Tensilica Technical Publications
-
Tensilica, Inc. 2011 Xtensa® LX4 microproscessor data book. Santa Clara, CA: Tensilica Technical Publications.
-
(2011)
Xtensa® LX4 Microproscessor Data Book
-
-
|