Implementing molecular dynamics on hybrid high performance computers - short range forces

[1]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[2]  Proceedings of the Physical Society , 1948, Nature.

[3]  Physical Review , 1965, Nature.

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

[5]  R. Hockney,et al.  Quiet high resolution computer models of a plasma , 1974 .

[6]  B. Berne Modification of the overlap potential to mimic a linear site-site potential , 1981 .

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

[8]  C. Zannoni,et al.  A generalized Gay-Berne intermolecular potential for biaxial particles , 1995 .

[9]  Lebowitz,et al.  Ellipsoid contact potential: Theory and relation to overlap potentials. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[10]  Gregory Bryan Computing in Science and Engineering , 1999, IEEE Software.

[11]  P. Drummond,et al.  Computer Physics Communications , 2001 .

[12]  L. Greengard,et al.  A new version of the fast multipole method for screened Coulomb interactions in three dimensions , 2002 .

[13]  Robert D. Skeel,et al.  Multiple grid methods for classical molecular dynamics , 2002, J. Comput. Chem..

[14]  Beat Ernst,et al.  Drug discovery today. , 2003, Current topics in medicinal chemistry.

[15]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[16]  Yunfei Chen,et al.  GPU accelerated molecular dynamics simulation of thermal conductivities , 2007, J. Comput. Phys..

[17]  S. Meloni,et al.  Efficient particle labeling in atomistic simulations. , 2007, The Journal of chemical physics.

[18]  Klaus Schulten,et al.  GPU acceleration of cutoff pair potentials for molecular modeling applications , 2008, CF '08.

[19]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[20]  A. Arnold,et al.  Harvesting graphics power for MD simulations , 2007, 0709.3225.

[21]  Steven J. Plimpton,et al.  Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics , 2008, Comput. Phys. Commun..

[22]  Weiguo Liu,et al.  Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA , 2008, Comput. Phys. Commun..

[23]  M J Harvey,et al.  The impact of accelerator processors for high-throughput molecular modeling and simulation. , 2008, Drug discovery today.

[24]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[25]  Matt K. Petersen,et al.  Liquid crystal nanodroplets in solution. , 2009, The Journal of chemical physics.

[26]  Ümit V. Çatalyürek,et al.  Investigating the use of GPU-accelerated nodes for SAR image formation , 2009, 2009 IEEE International Conference on Cluster Computing and Workshops.

[27]  Michael Garland,et al.  Designing efficient sorting algorithms for manycore GPUs , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[28]  Klaus Schulten,et al.  Multilevel summation of electrostatic potentials using graphics processing units , 2009, Parallel Comput..

[29]  M J Harvey,et al.  ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. , 2009, Journal of chemical theory and computation.

[30]  Bill Howe,et al.  2009 IEEE International Conference on Cluster Computing and Workshops , 2009, Cluster 2009.

[31]  M J Harvey,et al.  An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. , 2009, Journal of chemical theory and computation.

[32]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[33]  John E. Stone,et al.  OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems , 2010, Computing in Science & Engineering.

[34]  Sadaf R. Alam,et al.  Towards microsecond biological molecular dynamics simulations on hybrid processors , 2010, 2010 International Conference on High Performance Computing & Simulation.

[35]  Wilfred F. van Gunsteren,et al.  A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software , 2010, J. Comput. Chem..

[36]  Vijay S. Pande,et al.  Efficient nonbonded interactions for molecular dynamics on a graphics processing unit , 2010, J. Comput. Chem..

[37]  Eric F Darve,et al.  Author ' s personal copy A hybrid method for the parallel computation of Green ’ s functions , 2009 .

[38]  Journal of Chemical Physics , 1932, Nature.