Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program

We report our work to parallelize the Particle Mesh Ewald (PME) method to compute the long-range electrostatic interactions in the molecular dynamics program AMBER and to extend the scalability of the PME method to hundreds of processors.

[1]  A. D. de Vos,et al.  The Ca2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. , 1994, Biochemistry.

[2]  H. Schreiber,et al.  Molecular dynamics studies of solvated polypeptides: Why the cut-off scheme does not work , 1992 .

[3]  Edmund Bertschinger,et al.  Particle-Mesh Methods On The Connection Machine , 1994 .

[4]  Lee G. Pedersen,et al.  Characterization of γ-Carboxyglutamic Acid Residue 21 of Human Factor IX† , 1996 .

[5]  M. Prueitt.  Computer Simulation of Molecular Dynamics. , 1971 .

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

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

[8]  Bernard R. Brooks,et al.  New spherical‐cutoff methods for long‐range forces in macromolecular simulation , 1994, J. Comput. Chem..

[9]  N Hamaguchi,et al.  Characterization of gamma-carboxyglutamic acid residue 21 of human factor IX. , 1996, Biochemistry.

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

[11]  L. Li,et al.  Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm. , 1997, Biochemistry.

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

[13]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[14]  I. J. Schoenberg.  Cardinal Spline Interpolation , 1987 .

[15]  Jim Glosli,et al.  Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems , 1996 .

[16]  Kenneth M. Merz,et al.  A highly portable parallel implementation of AMBER4 using the message passing interface standard , 1995, J. Comput. Chem..

[17]  Peter A. Kollman,et al.  AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .