Scalable parallel molecular dynamics algorithms for organic systems

[1]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[2]  D. E. Parry The electrostatic potential in the surface region of an ionic crystal , 1975 .

[3]  L. h. Yang,et al.  A Linked-Cell Domain Decomposition Method for Molecular Dynamics Simulation on a Scalable Multiprocessor , 1992, Sci. Program..

[4]  Makoto Haraguchi,et al.  Parallel molecular dynamics simulation of a protein , 2001, Parallel Comput..

[5]  J. Perram,et al.  Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants , 1980, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[6]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[7]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[8]  A. Nakano,et al.  Multiresolution molecular dynamics algorithm for realistic materials modeling on parallel computers , 1994 .

[9]  G. R. Smith,et al.  Simulations of ion channels--watching ions and water move. , 2000, Trends in biochemical sciences.

[10]  Aiichiro Nakano Multiresolution load balancing in curved space: the wavelet representation , 1999 .

[11]  Farid F. Abraham,et al.  Portrait of a crack: rapid fracture mechanics using parallel molecular dynamics , 1997 .

[12]  Timothy Campbell,et al.  An Adaptive Curvilinear-Coordinate Approach to Dynamic Load Balancing of Parallel Multiresolution Molecular Dynamics , 1997, Parallel Comput..

[13]  M. Berkowitz,et al.  Ewald summation for systems with slab geometry , 1999 .

[14]  Frederick H. Streitz,et al.  Electrostatic potentials for metal-oxide surfaces and interfaces. , 1994 .

[15]  Giovanni Ciccotti,et al.  Molecular dynamics simulation of rigid molecules , 1986 .

[16]  Laxmikant V. Kalé,et al.  NAMD: Biomolecular Simulation on Thousands of Processors , 2002, ACM/IEEE SC 2002 Conference (SC'02).

[17]  Subhash Saini,et al.  Scalability of a low-cost multi-Teraflop Linux cluster for high-end classical atomistic and quantum mechanical simulations , 2003, Proceedings International Parallel and Distributed Processing Symposium.

[18]  C. Brooks,et al.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.

[19]  Leslie Greengard,et al.  A fast algorithm for particle simulations , 1987 .

[20]  J. Trent,et al.  Ordered nanoparticle arrays formed on engineered chaperonin protein templates , 2002, Nature materials.

[21]  Klaus Schulten,et al.  Mechanical unfolding intermediates in titin modules , 1999, Nature.

[22]  Martin Head-Gordon,et al.  Derivation and efficient implementation of the fast multipole method , 1994 .

[23]  D. Y. Yoon,et al.  Force field for simulations of 1,2-dimethoxyethane and poly(oxyethylene) based upon ab initio electronic structure calculations on model molecules , 1993 .

[24]  A. Nakano,et al.  Role of atomic charge transfer on sintering of TiO2 nanoparticles: Variable-charge molecular dynamics , 2000 .

[25]  Mark E. Tuckerman,et al.  Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers , 2000 .

[26]  Jack J. Dongarra,et al.  Performance of various computers using standard linear equations software in a FORTRAN environment , 1988, CARN.

[27]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

[28]  Mark E. Tuckerman,et al.  Explicit reversible integrators for extended systems dynamics , 1996 .

[29]  T. Darden,et al.  A Multipole-Based Algorithm for Efficient Calculation of Forces and Potentials in Macroscopic Period , 1996 .

[30]  Subhash Saini,et al.  Scalable atomistic simulation algorithms for materials research , 2002 .

[31]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[32]  D. C. Rapaport,et al.  The Art of Molecular Dynamics Simulation , 1997 .

[33]  J. Perram,et al.  Electrostatic lattice sums for semi-infinite lattices , 1979 .

[34]  Michael W. Deem,et al.  The h = 0 term in Coulomb sums by the Ewald transformation , 1990 .

[35]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[36]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[37]  Anthony Skjellum,et al.  Using MPI - portable parallel programming with the message-parsing interface , 1994 .

[38]  L. Verlet Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[39]  Peter S. Lomdahl,et al.  Recent advances in large-scale atomistic materials simulations , 1999, Comput. Sci. Eng..

[40]  Rajiv K. Kalia,et al.  DYNAMICS OF OXIDATION OF ALUMINUM NANOCLUSTERS USING VARIABLE CHARGE MOLECULAR-DYNAMICS SIMULATIONS ON PARALLEL COMPUTERS , 1999 .

[41]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[42]  R. J. Doerksen,et al.  De novo design of biomimetic antimicrobial polymers , 2002, Proceedings of the National Academy of Sciences of the United States of America.