-
3
-
-
0029979312
-
Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study
-
Feb
-
Z. R. Wasserman and C. N. Hodge, "Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study", J. Proteins: Structure, Function, and Bioinformatics, vol. 24, no. 2, pp. 227-237, Feb. 1996.
-
(1996)
J. Proteins: Structure, Function, and Bioinformatics
, vol.24
, Issue.2
, pp. 227-237
-
-
Wasserman, Z.R.1
Hodge, C.N.2
-
4
-
-
0030157593
-
A structural and energetics analysis of the binding of a series of N-acetylneuraminicacid-based inhibitors to influenza virus sialidase
-
June
-
N. R. Taylor and M. Itzstein, "A structural and energetics analysis of the binding of a series of N-acetylneuraminicacid-based inhibitors to influenza virus sialidase", J. Computer-Aided Molecular Design, vol. 10, no. 3, pp. 233-246, June 1996.
-
(1996)
J. Computer-Aided Molecular Design
, vol.10
, Issue.3
, pp. 233-246
-
-
Taylor, N.R.1
Itzstein, M.2
-
5
-
-
0030586030
-
The first step in sugar transport: Crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: Sugar phosphotransferase system and a model of the phosphotransfer complex with HPr
-
July
-
D. I. Liao, E. Silverton, Y. J. Seok, B. R. Lee, A. Peterkofsky and D. R. Davies, "The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.", J. Structure, vol. 4, no. 7, pp. 861-872, July 1996.
-
(1996)
J. Structure
, vol.4
, Issue.7
, pp. 861-872
-
-
Liao, D.I.1
Silverton, E.2
Seok, Y.J.3
Lee, B.R.4
Peterkofsky, A.5
Davies, D.R.6
-
6
-
-
0030585428
-
Solution structure of the donor site of a transsplicing RNA
-
June
-
N. L. Greenbaum, I. Radhakrishnan, D. J. Patel and D. Hirsh, "Solution structure of the donor site of a transsplicing RNA", J. Structure, vol. 4, no. 6, pp. 725-733, June 1996.
-
(1996)
J. Structure
, vol.4
, Issue.6
, pp. 725-733
-
-
Greenbaum, N.L.1
Radhakrishnan, I.2
Patel, D.J.3
Hirsh, D.4
-
8
-
-
84977266737
-
Evaluation of optical and electrostatic lattice potentials
-
P. P. Ewald, "Evaluation of optical and electrostatic lattice potentials", Ann. Phys Leipzig, vol. 64, pp. 253-287, 1921.
-
(1921)
Ann. Phys Leipzig
, vol.64
, pp. 253-287
-
-
Ewald, P.P.1
-
9
-
-
22944467757
-
Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
-
July
-
L. Verlet, "Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules", Physical Review, vol. 159, no. 1, pp. 98-103, July 1967.
-
(1967)
Physical Review
, vol.159
, Issue.1
, pp. 98-103
-
-
Verlet, L.1
-
10
-
-
0000394426
-
Some Multistep Methods for Use in Molecular Dynamics Calculations
-
Feb
-
D. Beeman, "Some Multistep Methods for Use in Molecular Dynamics Calculations", J. Computational Physics, vol. 20, pp. 130-139, Feb. 1976.
-
(1976)
J. Computational Physics
, vol.20
, pp. 130-139
-
-
Beeman, D.1
-
11
-
-
33646650705
-
Reversible multiple time-scale molecular dynamics
-
March
-
M.E. Tuckerman, G.J. Martyna and B.J. Berne, "Reversible multiple time-scale molecular dynamics", J. Chemical Physics, vol. 97, no. 3, pp. 1990-2001, March 1992.
-
(1992)
J. Chemical Physics
, vol.97
, Issue.3
, pp. 1990-2001
-
-
Tuckerman, M.E.1
Martyna, G.J.2
Berne, B.J.3
-
12
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Oct
-
D. V. D. Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. Berendsen, "GROMACS: Fast, flexible, and free", J. Computational Chemistry, vol. 26, no. 16, pp. 1701-1718, Oct. 2005.
-
(2005)
J. Computational Chemistry
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Spoel, D.V.D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
13
-
-
84860996170
-
-
GROMACS-4.0.7, available at, Dec
-
GROMACS-4.0.7, "Download website for GROMACS 4.0.7", available at http://www.gromacs.org, Dec. 2009.
-
(2009)
Download Website for GROMACS 4.0.7
-
-
-
14
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Oct
-
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale and K. Schulten, "Scalable molecular dynamics with NAMD", J. Computational Chemistry, vol. 26., no. 16, pp. 1781-1802, Oct. 2005.
-
(2005)
J. 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
-
15
-
-
84861005048
-
-
NAMD-2.7b2, available at, Nov
-
NAMD-2.7b2, "Download website for NAMD 2.7b2", available at http://www.ks.uiuc.edu/Research/namd, Nov. 2009.
-
(2009)
Download Website for NAMD 2.7b2
-
-
-
16
-
-
84861005047
-
-
LAMMPS, available at, Jan
-
LAMMPS, "Download website for LAMMPS", available at http://lammps.sandia.gov, Jan. 2010.
-
(2010)
Download Website for LAMMPS
-
-
-
17
-
-
33749169503
-
A highly parallelized special-purpose computer for many-body simulations with an arbitrary central force: MD-GRAPE
-
Sep
-
F. Toshiyuki, T. Makoto, M. Junichiro, E. Toshikazu and S. Duiichiro, "A Highly Parallelized Special-Purpose Computer for Many-Body Simulations with an Arbitrary Central Force: MD-GRAPE", Astrophysical Journal, vol. 468, pp. 51-61, Sep. 1996.
-
(1996)
Astrophysical Journal
, vol.468
, pp. 51-61
-
-
Toshiyuki, F.1
Makoto, T.2
Junichiro, M.3
Toshikazu, E.4
Duiichiro, S.5
-
18
-
-
0001489848
-
Fast and accurate molecular dynamics sumulation of a protein using a special-purpose computer
-
Sep
-
Y. Komeiji, M. Uebayasi, R. Takata, A. Shimizu, K. Itsukashi and M. Taiji, "Fast and Accurate Molecular Dynamics Sumulation of a Protein Using a Special-Purpose Computer", J. Computational Chemistry, vol. 18, no. 12, pp. 1546-1563, Sep. 1997.
-
(1997)
J. Computational Chemistry
, vol.18
, Issue.12
, pp. 1546-1563
-
-
Komeiji, Y.1
Uebayasi, M.2
Takata, R.3
Shimizu, A.4
Itsukashi, K.5
Taiji, M.6
-
19
-
-
0001700958
-
Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations
-
S. Toyoda, H. Miyagawa, K. Kitamura, T. Amisaki, E. Hashimoto, H. Ikeda, A. Kusumi and N. Miyakawa, "Development of MD Engine: High-Speed Accelerator with Parallel Processor Design for Molecular Dynamics Simulations", J. Computational Chemistry, vol. 20, no.2, pp. 185-199, 1999.
-
(1999)
J. 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
-
22
-
-
44049100960
-
Accelerating molecular dynamics simulations with reconfigurable computers
-
June
-
R. Scrofano, M. B. Gokhale, F. Trouw and V. K. Prasanna, "Accelerating Molecular Dynamics Simulations with Reconfigurable Computers", IEEE Trans. on Parallel and Distributed Systems, vol. 19, no. 6, pp. 764-778, June 2008.
-
(2008)
IEEE Trans. on Parallel and Distributed Systems
, vol.19
, Issue.6
, pp. 764-778
-
-
Scrofano, R.1
Gokhale, M.B.2
Trouw, F.3
Prasanna, V.K.4
-
24
-
-
43049179828
-
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
-
May
-
Y. Gu, T. VanCourt and M. C. Herbordt, "Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations", Elsevier Parallel Computing, vol. 34, no. 4, pp. 261-277, May 2008.
-
(2008)
Elsevier Parallel Computing
, vol.34
, Issue.4
, pp. 261-277
-
-
Gu, Y.1
vanCourt, T.2
Herbordt, M.C.3
-
25
-
-
18644385256
-
Reconfigurable Molecular Dynamics Simulator
-
Apr
-
N. Azizi, I. Kuon, A. Egier, A. Darabiha and P. Chow, "Reconfigurable Molecular Dynamics Simulator", Proc. IEEE Symp. Field-Programmable Custom Computing Machines, pp. 197-206, Apr. 2004.
-
(2004)
Proc. IEEE Symp. Field-Programmable Custom Computing Machines
, pp. 197-206
-
-
Azizi, N.1
Kuon, I.2
Egier, A.3
Darabiha, A.4
Chow, P.5
-
27
-
-
84861004361
-
-
LAMMPS, available at, Jan
-
LAMMPS, "LAMMPS manual", available at http://lammps.sandia.gov/doc/Manual.html, Jan. 2010.
-
(2010)
LAMMPS Manual
-
-
-
28
-
-
0000396658
-
A Fast Algorithm for Particle Simulations
-
Dec
-
L. Greengard and V. Rokhlin, "A Fast Algorithm for Particle Simulations", J. Computational Physics, vol. 73, no.2, pp. 325-348, Dec. 1987.
-
(1987)
J. Computational Physics
, vol.73
, Issue.2
, pp. 325-348
-
-
Greengard, L.1
Rokhlin, V.2
-
29
-
-
5244247401
-
Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions
-
Sep
-
H. Q. Ding, N. Karasawa and W. A. Goddard, "Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions", J. Chemical Physics, vol. 97, no. 6, pp. 4309-4315, Sep. 1992.
-
(1992)
J. Chemical Physics
, vol.97
, Issue.6
, pp. 4309-4315
-
-
Ding, H.Q.1
Karasawa, N.2
Goddard, W.A.3
-
31
-
-
33846823909
-
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
-
June
-
T. Darden, D. York and L. Pedersen, "Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems", J. Chemical Physics, vol. 98, no. 12, pp. 10089-10092, June 1993.
-
(1993)
J. Chemical Physics
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
32
-
-
0002467378
-
Fast Parallel Algorithms for Short-Range Molecular Dynamics
-
Mar
-
S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J. Computational Physics, vol. 117, no. 1, pp. 1-19, Mar. 1995.
-
(1995)
J. Computational Physics
, vol.117
, Issue.1
, pp. 1-19
-
-
Plimpton, S.1
-
34
-
-
0030172529
-
Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems
-
June
-
E. L. Pollock and J. Glosli, "Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems", Computer Physics Communications, vol. 95, no. 2, pp. 93-110, June 1996.
-
(1996)
Computer Physics Communications
, vol.95
, Issue.2
, pp. 93-110
-
-
Pollock, E.L.1
Glosli, J.2
-
35
-
-
50949119436
-
Maxwell-a 64 FPGA supercputer
-
R. Baxter, S. Booth, M. Bull, G. Cawood, J. Perry, M. Parsons, A. Simpson, A. Trew, A. McCormick, G. Smart, R.Smart, A. Cantle, R. Chamberlain and G. Genest, "Maxwell-a 64 FPGA supercputer", Proc. NASA/ESA Conf. Adaptive Hardware Systems, pp. 287-294, 2007.
-
(2007)
Proc. NASA/ESA Conf. Adaptive Hardware Systems
, pp. 287-294
-
-
Baxter, R.1
Booth, S.2
Bull, M.3
Cawood, G.4
Perry, J.5
Parsons, M.6
Simpson, A.7
Trew, A.8
McCormick, A.9
Smart, G.10
Smart, R.11
Cantle, A.12
Chamberlain, R.13
Genest, G.14
-
36
-
-
84860996172
-
-
FHPCA, Edinburgh, U.K, available at
-
FHPCA, Edinburgh, U.K., "The FHPCA website", available at http://www.fhpca.org, 2010.
-
(2010)
The FHPCA Website
-
-
-
37
-
-
84861005050
-
-
Alpha Data Ltd., Edinburgh, U.K, available at, May
-
Alpha Data Ltd., Edinburgh, U.K., "ADM-XRC-4FX Datasheet", available at http://www.alphadata.co.uk./admadm-xrc-4fx.html, May 2007.
-
(2007)
ADM-XRC-4FX Datasheet
-
-
-
38
-
-
84861005051
-
-
Nallatech Ltd., Glasgow, U.K, available at, May
-
Nallatech Ltd., Glasgow, U.K., "H100 Series Datasheet", available at http://www.nallatech.com/meadiLibrary/images/english/5595.pdf, May 2007.
-
(2007)
H100 Series Datasheet
-
-
-
39
-
-
50949133605
-
The FPGA HPC alliance parallel toolkit
-
R. Baxter, S. Booth, M. Bull, G. Cawood, J. Perry, M. Parsons, A. Simpson, A. Trew, A. McCormick, G. Smart, R. Smart, A. Cantle, R. Chamberlain and G. Genest, "The FPGA HPC alliance parallel toolkit", Proc. NASA/ESA Conf. Adaptive Hardware Systems, pp.301-310, 2007.
-
(2007)
Proc. NASA/ESA Conf. Adaptive Hardware Systems
, pp. 301-310
-
-
Baxter, R.1
Booth, S.2
Bull, M.3
Cawood, G.4
Perry, J.5
Parsons, M.6
Simpson, A.7
Trew, A.8
McCormick, A.9
Smart, G.10
Smart, R.11
Cantle, A.12
Chamberlain, R.13
Genest, G.14
-
40
-
-
84861008637
-
-
FHPCA, Edinburgh, U.K, available at, Mar
-
FHPCA, Edinburgh, U.K., "PowerPoint presentation", available at http://www.fhpca.org/download/MRSC07-Mar07.ppt, Mar. 2007.
-
(2007)
PowerPoint Presentation
-
-
-
41
-
-
84861013600
-
-
Argonne National Lab, Argonne, IL, avail able at
-
Argonne National Lab, Argonne, IL, "MPI manual", avail able at http://www.unix.mcs.anl.gov/mpi/www/www3/MPI_Wtime.html, 2009.
-
(2009)
MPI Manual
-
-
-
42
-
-
84861005538
-
-
OpenCores website, available at
-
OpenCores website, "Floating Point Adder and Multiplier", available at http://opencores.org/project,fpuvhdl, 2009.
-
(2009)
Floating Point Adder and Multiplier
-
-
-
43
-
-
28444450481
-
A Fully Synthesizable Single-Precision, Floating-Point Adder/ Subtractor and Multiplier in VHDL for General and Educational Use
-
Nov
-
G. Marcus, P. Hinojosa, A. Avila and J. N. Flores, "A Fully Synthesizable Single-Precision, Floating-Point Adder/ Subtractor and Multiplier in VHDL for General and Educational Use", Proc. IEEE International Caracas Conf. Devices, Circuits and Systems, pp. 319-323, Nov. 2004.
-
(2004)
Proc. IEEE International Caracas Conf. Devices, Circuits and Systems
, pp. 319-323
-
-
Marcus, G.1
Hinojosa, P.2
Avila, A.3
Flores, J.N.4
-
44
-
-
84861000437
-
-
Xilinx Inc., San Jose, CA, available at, May
-
Xilinx Inc., San Jose, CA, "Virtex-4 datasheets", available at http://www.xilinx.com/products/silicon_solutions/fpgas/virtex/virtex4/index.htm, May 2007.
-
(2007)
Virtex-4 Datasheets
-
-
-
45
-
-
84986471218
-
Error evaluation in the design of a specialpurpose processor that calculates nonbonded forces in molecular dynamics simulations
-
Sep
-
T. Amisaki, T. Fujiwara, A. Kusumi, H. Miyagawa and K. Kitamura, "Error evaluation in the design of a specialpurpose processor that calculates nonbonded forces in molecular dynamics simulations", J. Computational Chemistry, vol. 16, no. 9, pp. 1120-1130, Sep. 1995.
-
(1995)
J. Computational Chemistry
, vol.16
, Issue.9
, pp. 1120-1130
-
-
Amisaki, T.1
Fujiwara, T.2
Kusumi, A.3
Miyagawa, H.4
Kitamura, K.5
-
47
-
-
33846844133
-
A case study in porting a production scientific supercomputing application to a reconfigurable computer
-
April
-
V. Kindratenko, D. Pointer, "A case study in porting a production scientific supercomputing application to a reconfigurable computer", Proc. IEEE Symp. Field-Programmable Custom Computing Machines, pp. 13-22, April 2006.
-
(2006)
Proc. IEEE Symp. Field-Programmable Custom Computing Machines
, pp. 13-22
-
-
Kindratenko, V.1
Pointer, D.2
|