Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems
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Haruki Nakamura | Ryutaro Himeno | Makoto Taiji | Narutoshi Kamiya | Yasushige Yonezawa | Rossen Apostolov | Gota Kikugawa | Haruki Nakamura | M. Taiji | R. Himeno | N. Kamiya | Y. Yonezawa | G. Kikugawa | R. Apostolov
[1] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[2] S. Phillpot,et al. Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r−1 summation , 1999 .
[3] Bernard R. Brooks,et al. New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..
[4] Y. Fukunishi,et al. The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking , 2003 .
[5] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[6] J. D. Gezelter,et al. Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. , 2006, The Journal of chemical physics.
[7] Y Ma,et al. Application of the Wolf damped Coulomb method to simulations of SiC. , 2005, The Journal of chemical physics.
[8] J. W. Causey,et al. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm , 1992 .
[9] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[10] Makino,et al. Astrophysics on the GRAPE family of special-purpose computers , 1999, Science.
[11] Pierfranco Demontis,et al. Application of the Wolf method for the evaluation of Coulombic interactions to complex condensed matter systems: Aluminosilicates and water , 2001 .
[12] W. Goddard,et al. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .
[13] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[14] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[15] Haruki Nakamura,et al. Molecular dynamics study on mobility and dipole ordering of solvent around proteins: effects of periodic-box size and protein charge , 1999 .
[16] Yoshiteru Yonetani,et al. A severe artifact in simulation of liquid water using a long cut-off length: Appearance of a strange layer structure , 2005 .
[17] Toshikazu Ebisuzaki,et al. Hardware accelerator for molecular dynamics: MDGRAPE-2 , 2003 .
[18] Stefan M. Kast,et al. Enhancement of the wolf damped Coulomb potential: Static, dynamic, and dielectric properties of liquid water from molecular simulation , 2002 .
[19] Alejandro Gil-Villegas,et al. Monte Carlo simulations of primitive models for ionic systems using the Wolf method , 2006 .