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Volumn 230, Issue 24, 2011, Pages 8744-8761

Spectral accuracy in fast Ewald-based methods for particle simulations

Author keywords

Ewald summation; FFT; Molecular dynamics; PME; Spectral accuracy; SPME

Indexed keywords

ERRORS; FAST FOURIER TRANSFORMS; FREQUENCY DOMAIN ANALYSIS;

EID: 80053628839     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2011.08.022     Document Type: Article
Times cited : (67)

References (39)
  • 1
    • 33645981305 scopus 로고    scopus 로고
    • Electrostatics calculations: latest methodological advances
    • Koehl P. Electrostatics calculations: latest methodological advances. Curr. Opin. Struc. Biol. 2006, 16:142-151.
    • (2006) Curr. Opin. Struc. Biol. , vol.16 , pp. 142-151
    • Koehl, P.1
  • 2
    • 84977266737 scopus 로고
    • Die berechnung optischer und elektrostatischer gitterpotentiale
    • Ewald P. Die berechnung optischer und elektrostatischer gitterpotentiale. Ann. Phys. 1921, 64:253-287.
    • (1921) Ann. Phys. , vol.64 , pp. 253-287
    • Ewald, P.1
  • 3
    • 0344775414 scopus 로고    scopus 로고
    • Direct sum of coulomb potential without ambiguities of conditionally convergent series
    • Takemoto H., Ohyama T., Tohsaki A. Direct sum of coulomb potential without ambiguities of conditionally convergent series. Progress of Theoretical Physics 2003, 109(4):563-573.
    • (2003) Progress of Theoretical Physics , vol.109 , Issue.4 , pp. 563-573
    • Takemoto, H.1    Ohyama, T.2    Tohsaki, A.3
  • 5
    • 33846823909 scopus 로고
    • Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems
    • Darden T., York D., Pedersen L. Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 7
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl E., Hess B., van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7:306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 8
    • 85190085855 scopus 로고    scopus 로고
    • Gromacs homepage URL
    • Gromacs homepage (2010). URL http://www.gromacs.org/.
    • (2010)
  • 10
    • 85190073152 scopus 로고    scopus 로고
    • Amber molecular dynamics package. URL .
    • Amber molecular dynamics package (2010). URL http://ambermd.org/.
    • (2010)
  • 12
    • 85190071505 scopus 로고    scopus 로고
    • NAMD scalable molecular dynamics. URL
    • NAMD scalable molecular dynamics (2010). URL http://www.ks.uiuc.edu/Research/namd/.
    • (2010)
  • 13
    • 22244433235 scopus 로고    scopus 로고
    • How to mesh up Ewald sums. I.A theoretical and numerical comparison of various particle mesh routines
    • Deserno M., Holm C. How to mesh up Ewald sums. I.A theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys. 1998, 109:7678-7693.
    • (1998) J. Chem. Phys. , vol.109 , pp. 7678-7693
    • Deserno, M.1    Holm, C.2
  • 15
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4:435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 16
    • 0035870662 scopus 로고    scopus 로고
    • Multigrid methods for classical molecular dynamics simulations of biomolecules
    • Sagui C., Darden T. Multigrid methods for classical molecular dynamics simulations of biomolecules. J. Chem. Phys. 2001, 114:6578-6591.
    • (2001) J. Chem. Phys. , vol.114 , pp. 6578-6591
    • Sagui, C.1    Darden, T.2
  • 17
    • 0037197257 scopus 로고    scopus 로고
    • Multiple grid methods for classical molecular dynamics
    • Skeel R., Tezcan I., Hardy D. Multiple grid methods for classical molecular dynamics. J. Comput. Chem. 2002, 23:673-684.
    • (2002) J. Comput. Chem. , vol.23 , pp. 673-684
    • Skeel, R.1    Tezcan, I.2    Hardy, D.3
  • 18
    • 22944460220 scopus 로고    scopus 로고
    • Gaussian split Ewald: a fast Ewald mesh method for molecular simulation
    • Shan Y., Klepeis J., Eastwood M., Dror R., Shaw D. Gaussian split Ewald: a fast Ewald mesh method for molecular simulation. J. Chem. Phys. 2005, 122:054101.
    • (2005) J. Chem. Phys. , vol.122 , pp. 054101
    • Shan, Y.1    Klepeis, J.2    Eastwood, M.3    Dror, R.4    Shaw, D.5
  • 19
    • 4444328799 scopus 로고    scopus 로고
    • Efficient computation of long-range electromagnetic interactions without Fourier transforms
    • Tsukerman I. Efficient computation of long-range electromagnetic interactions without Fourier transforms. IEEE Trans. Mag. 2004, 40:2158-2160.
    • (2004) IEEE Trans. Mag. , vol.40 , pp. 2158-2160
    • Tsukerman, I.1
  • 20
    • 77950162689 scopus 로고    scopus 로고
    • Multi-level Ewald: a hybrid multigrid/fast fourier transform approach to the electrostatic particle-mesh problem
    • Cerutti D.S., Case D.A. Multi-level Ewald: a hybrid multigrid/fast fourier transform approach to the electrostatic particle-mesh problem. J. Chem. Theory Comput. 2010, 6(2):443-458.
    • (2010) J. Chem. Theory Comput. , vol.6 , Issue.2 , pp. 443-458
    • Cerutti, D.S.1    Case, D.A.2
  • 21
    • 73349131117 scopus 로고    scopus 로고
    • Staggered mesh ewald: an extension of the smooth particle-mesh ewald method adding great versatility
    • Cerutti D.S., Duke R.E., Darden T.A., Lybrand T.P. Staggered mesh ewald: an extension of the smooth particle-mesh ewald method adding great versatility. J. Chem. Theory Comput. 2009, 5(9):2322-2338.
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.9 , pp. 2322-2338
    • Cerutti, D.S.1    Duke, R.E.2    Darden, T.A.3    Lybrand, T.P.4
  • 22
    • 15844377065 scopus 로고    scopus 로고
    • A smooth particle-mesh Ewald algorithm for Stokes suspension simulations: The sedimentation of fibers
    • Saintillan D., Darve E., Shaqfeh E. A smooth particle-mesh Ewald algorithm for Stokes suspension simulations: The sedimentation of fibers. Phys. Fluids 2005, 17:033301.
    • (2005) Phys. Fluids , vol.17 , pp. 033301
    • Saintillan, D.1    Darve, E.2    Shaqfeh, E.3
  • 23
    • 77956947285 scopus 로고    scopus 로고
    • Spectrally accurate fast summation for periodic Stokes potentials
    • Lindbo D., Tornberg A.-K. Spectrally accurate fast summation for periodic Stokes potentials. J. Comput. Phys. 2010, 229:8994-9010.
    • (2010) J. Comput. Phys. , vol.229 , pp. 8994-9010
    • Lindbo, D.1    Tornberg, A.-K.2
  • 24
    • 0001298453 scopus 로고
    • Fast potential-theory .2. layer potentials and discrete sums
    • Strain J. Fast potential-theory .2. layer potentials and discrete sums. J. Comput. Phys. 1992, 99(2):251-270.
    • (1992) J. Comput. Phys. , vol.99 , Issue.2 , pp. 251-270
    • Strain, J.1
  • 25
    • 0001569292 scopus 로고
    • Cutoff errors in the Ewald summation formulas for point-charge systems
    • Kolafa J., Perram J. Cutoff errors in the Ewald summation formulas for point-charge systems. Mol. Simulat. 1992, 9:351-368.
    • (1992) Mol. Simulat. , vol.9 , pp. 351-368
    • Kolafa, J.1    Perram, J.2
  • 28
    • 0000091410 scopus 로고    scopus 로고
    • How to mesh up Ewald sums. II. An accurate error estimate for the particle-particle-particle-mesh algorithm
    • Deserno M., Holm C. How to mesh up Ewald sums. II. An accurate error estimate for the particle-particle-particle-mesh algorithm. J. Chem. Phys. 1998, 109:7694-7701.
    • (1998) J. Chem. Phys. , vol.109 , pp. 7694-7701
    • Deserno, M.1    Holm, C.2
  • 29
    • 4944230740 scopus 로고    scopus 로고
    • Accelerating the nonuniform fast Fourier transform
    • Greengard L., Lee J. Accelerating the nonuniform fast Fourier transform. SIAM Rev. 2004, 46(3):443-454.
    • (2004) SIAM Rev. , vol.46 , Issue.3 , pp. 443-454
    • Greengard, L.1    Lee, J.2
  • 30
    • 0000527817 scopus 로고
    • Fast Fourier-transforms for nonequispaced data
    • Dutt A., Rokhlin V. Fast Fourier-transforms for nonequispaced data. SIAM J. Sci. Comput. 1993, 14:1368-1393.
    • (1993) SIAM J. Sci. Comput. , vol.14 , pp. 1368-1393
    • Dutt, A.1    Rokhlin, V.2
  • 32
    • 78650734826 scopus 로고    scopus 로고
    • Efficiency of linked cell algorithms
    • Welling U., Germano G. Efficiency of linked cell algorithms. Comput. Phys. Commun. 2011, 182:611-615.
    • (2011) Comput. Phys. Commun. , vol.182 , pp. 611-615
    • Welling, U.1    Germano, G.2
  • 33
    • 85190080131 scopus 로고    scopus 로고
    • Gromacs user manual, version 4.5.4. URL
    • Gromacs user manual, version 4.5.4. URL http://ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf.
  • 35
    • 20444473641 scopus 로고    scopus 로고
    • MDSIMAID: automatic parameter optimization in fast electrostatic algorithms
    • Crocker M., Hampton S., Matthey T., Izaguirre J. MDSIMAID: automatic parameter optimization in fast electrostatic algorithms. J. Comput. Chem. 2005, 26(10):1021-1031. 10.1002/jcc.20240.
    • (2005) J. Comput. Chem. , vol.26 , Issue.10 , pp. 1021-1031
    • Crocker, M.1    Hampton, S.2    Matthey, T.3    Izaguirre, J.4
  • 37
    • 67849126626 scopus 로고    scopus 로고
    • A geometric nonuniform fast Fourier transform
    • Sammis I., Strain J. A geometric nonuniform fast Fourier transform. J. Comput. Phys. 2009, 228:7086-7108.
    • (2009) J. Comput. Phys. , vol.228 , pp. 7086-7108
    • Sammis, I.1    Strain, J.2
  • 38
    • 20744449792 scopus 로고    scopus 로고
    • The design and implementation of FFTW3
    • Frigo M., Johnson S.G. The design and implementation of FFTW3. P. IEEE 2005, 93:216-231.
    • (2005) P. IEEE , vol.93 , pp. 216-231
    • Frigo, M.1    Johnson, S.G.2
  • 39
    • 57049117343 scopus 로고    scopus 로고
    • How to write fast numerical code: a small introduction
    • Springer, Berlin / Heidelberg, Generative and Transformational Techniques in Software Engineering II
    • Chellappa S., Franchetti F., Pschel M. How to write fast numerical code: a small introduction. Lecture Notes in Computer Science 2008, Vol. 5235:196-259. Springer, Berlin / Heidelberg.
    • (2008) Lecture Notes in Computer Science , vol.5235 , pp. 196-259
    • Chellappa, S.1    Franchetti, F.2    Pschel, M.3


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