메뉴 건너뛰기




Volumn 9781461417910, Issue , 2013, Pages 105-135

FPGA-accelerated molecular dynamics

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL CHEMISTRY; COMPUTATIONAL EFFICIENCY; FIELD PROGRAMMABLE GATE ARRAYS (FPGA); INTEGRATED CIRCUIT DESIGN;

EID: 84949178335     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-1791-0_4     Document Type: Chapter
Times cited : (15)

References (50)
  • 1
    • 33646943202 scopus 로고    scopus 로고
    • Molecular dynamics: Survey of methods for simulating the activity of proteins
    • S.A. Adcock, J.A. McCammon, Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106(5), 1589-1615 (2006)
    • (2006) Chem. Rev , vol.106 , Issue.5 , pp. 1589-1615
    • Adcock, S.A.1    McCammon, J.A.2
  • 2
    • 41249087856 scopus 로고    scopus 로고
    • General purpose molecular dynamics simulations fully implemented on graphics processing units
    • J.A. Anderson, C.D. Lorenz, A. Travesset, General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 227(10), 5342-5359 (2008)
    • (2008) J. Comput. Phys , vol.227 , Issue.10 , pp. 5342-5359
    • Anderson, J.A.1    Lorenz, C.D.2    Travesset, A.3
  • 8
    • 77956007831 scopus 로고    scopus 로고
    • Molecular dynamics simulations on high-performance reconfigurable computing systems
    • M. Chiu,M.C. Herbordt, Molecular dynamics simulations on high-performance reconfigurable computing systems. ACM Trans. Reconfigurable Tech. Syst. (TRETS) 3(4), 23:1-23:37 (2010)
    • (2010) ACM Trans. Reconfigurable Tech. Syst. (TRETS) , vol.3 , Issue.4 , pp. 231-2337
    • Chiu, M.1    Herbordt, M.C.2
  • 11
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N.log (N) method for Ewald sums in large systems
    • T. Darden, D. York, L. Pedersen, Particle mesh Ewald: an N.log (N) method for Ewald sums in large systems. J. Chem. Phys. 98(12), 10089-10092 (1993)
    • (1993) J. Chem. Phys , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 13
    • 18144377695 scopus 로고    scopus 로고
    • Monitoring energy drift with shadow Hamiltonians
    • R.D. Engle, R.D. Skeel, M. Drees, Monitoring energy drift with shadow Hamiltonians. J. Comput. Phys. 206(2), 432-452 (2005)
    • (2005) J. Comput. Phys , vol.206 , Issue.2 , pp. 432-452
    • Engle, R.D.1    Skeel, R.D.2    Drees, M.3
  • 14
    • 33644848399 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the complete satellite tobacco mosaic virus
    • P.L. Freddolino, A.S. Arkhipov, S.B. Larson, A. McPherson, K. Schulten, Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14(3), 437-449 (2006)
    • (2006) Structure , vol.14 , Issue.3 , pp. 437-449
    • Freddolino, P.L.1    Arkhipov, A.S.2    Larson, S.B.3    McPherson, A.4    Schulten, K.5
  • 15
    • 85193189954 scopus 로고    scopus 로고
    • Accessed 17 April 2012
    • Gidel, Gidel website (2009), http://www.gidel.com. Accessed 17 April 2012
    • (2009) Gidel Website
  • 16
    • 85193180213 scopus 로고    scopus 로고
    • Accessed 17 April 2012
    • GROMACS, GROMACS installation instructions for GPUs (2012), http://www.gromacs.org/ Downloads/Installation Instructions/GPUs. Accessed 17 April 2012
    • (2012) GROMACS Installation Instructions for GPUs
  • 18
    • 43049179828 scopus 로고    scopus 로고
    • Explicit design of FPGA-based coprocessors for shortrange force computations in molecular dynamics simulations
    • Y. Gu, T. Vancourt, M.C. Herbordt, Explicit design of FPGA-based coprocessors for shortrange force computations in molecular dynamics simulations. Parallel Comput. 34(4-5), 261-277 (2008)
    • (2008) Parallel Comput , vol.34 , Issue.4-5 , pp. 261-277
    • Gu, Y.1    Vancourt, T.2    Herbordt, M.C.3
  • 19
    • 70049089977 scopus 로고    scopus 로고
    • University of Illinois at Urbana-Champaign. Accessed 17 April 2012
    • D.J. Hardy, NAMD-Lite (2007), http://www.ks.uiuc.edu/Development/MDTools/namdlite/. University of Illinois at Urbana-Champaign. Accessed 17 April 2012
    • (2007) NAMD-Lite
    • Hardy, D.J.1
  • 21
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput. 4(3), 435-447 (2008)
    • (2008) J. Chem. Theor. Comput , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Spoel Der D.Van3    Lindahl, E.4
  • 22
    • 0347784245 scopus 로고
    • Quiet high-resolution computer models of a plasma
    • R. Hockney, S. Goel, J. Eastwood, Quiet high-resolution computer models of a plasma. J. Comput. Phys. 14(2), 148-158 (1974)
    • (1974) J. Comput. Phys , vol.14 , Issue.2 , pp. 148-158
    • Hockney, R.1    Goel, S.2    Eastwood, J.3
  • 24
    • 80052133904 scopus 로고    scopus 로고
    • A high performance implementation for molecular dynamics simulations on a FPGA supercomputer
    • IEEE Computer Society Washington, DC, USA
    • S. Kasap, K. Benkrid, A high performance implementation for molecular dynamics simulations on a FPGA supercomputer, in 2011 NASA/ESA Conference on Adaptive Hardware and Systems (AHS) (2011), IEEE Computer Society Washington, DC, USA, pp. 375-382
    • (2011) 2011 NASA/ESA Conference on Adaptive Hardware and Systems (AHS) , pp. 375-382
    • Kasap, S.1    Benkrid, K.2
  • 25
  • 26
    • 33846844133 scopus 로고    scopus 로고
    • A case study in porting a production scientific supercomputing application to a reconfigurable computer
    • IEEE Computer Society Washington, DC, USA
    • V. Kindratenko, D. Pointer, A case study in porting a production scientific supercomputing application to a reconfigurable computer, in 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM) (2006), IEEE Computer Society Washington, DC, USA, pp. 13-22
    • (2006) 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM) , pp. 13-22
    • Kindratenko, V.1    Pointer, D.2
  • 30
    • 0242593434 scopus 로고    scopus 로고
    • Development and current status of the CHARMM force field for nucleic acids
    • A.D. MacKerell, N. Banavali, N. Foloppe, Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56(4), 257-265 (2000)
    • (2000) Biopolymers , vol.56 , Issue.4 , pp. 257-265
    • Mackerell, A.D.1    Banavali, N.2    Foloppe, N.3
  • 33
    • 67650135820 scopus 로고    scopus 로고
    • Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations
    • L. Nilsson, Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations. J. Comput. Chem. 30(9), 1490-1498 (2009)
    • (2009) J. Comput. Chem , vol.30 , Issue.9 , pp. 1490-1498
    • Nilsson, L.1
  • 37
    • 0002467378 scopus 로고
    • Fast parallel algorithms for short-range molecular dynamics
    • S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117(1), 1-19 (1995)
    • (1995) J. Comput. Phys , vol.117 , Issue.1 , pp. 1-19
    • Plimpton, S.1
  • 38
    • 0242443693 scopus 로고    scopus 로고
    • Force fields for protein simulations
    • J.W. Ponder, D.A. Case, Force fields for protein simulations. Adv. Protein Chem. 66, 27-85 (2003)
    • (2003) Adv. Protein Chem , vol.66 , pp. 27-85
    • Ponder, J.W.1    Case, D.A.2
  • 40
    • 0041559073 scopus 로고
    • Computer simulation studies of the liquid state
    • P. Schofield, Computer simulation studies of the liquid state. Comp. Phys. Comm. 5(1), 17-23 (1973)
    • (1973) Comp. Phys. Comm , vol.5 , Issue.1 , pp. 17-23
    • Schofield, P.1
  • 42
    • 22944460220 scopus 로고    scopus 로고
    • Gaussian split Ewald: A fast Ewald mesh method for molecular simulation
    • Y. Shan, J. Klepeis, M. Eastwood, R. Dror, D. Shaw, Gaussian split Ewald: a fast Ewald mesh method for molecular simulation. J. Chem. Phys. 122(5), 54101:1-54101:13 (2005)
    • (2005) J. Chem. Phys , vol.122 , Issue.5 , pp. 541011-54113
    • Shan, Y.1    Klepeis, J.2    Eastwood, M.3    Dror, R.4    Shaw, D.5
  • 46
    • 0037197257 scopus 로고    scopus 로고
    • Multiple grid methods for classical molecular dynamics
    • R.D. Skeel, I. Tezcan, D.J. Hardy, Multiple grid methods for classical molecular dynamics. J. Comput. Chem. 23(6), 673-684 (2002)
    • (2002) J. Comput. Chem , vol.23 , Issue.6 , pp. 673-684
    • Skeel, R.D.1    Tezcan, I.2    Hardy, D.J.3
  • 47
    • 1642632943 scopus 로고    scopus 로고
    • A note on N-body computations with cutoffs
    • M. Snir, A note on N-body computations with cutoffs. Theor. Comput. Syst. 37(2), 295-318 (2004)
    • (2004) Theor. Comput. Syst , vol.37 , Issue.2 , pp. 295-318
    • Snir, M.1
  • 49
    • 22944467757 scopus 로고
    • Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
    • L. Verlet, Computer "Experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159(1), 98-103 (1967)
    • (1967) Phys. Rev , vol.159 , Issue.1 , pp. 98-103
    • Verlet, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.