OOMPAA-Object-Oriented Model for Probing Assemblages of Atoms

An object-oriented library is presented for building molecular-modeling software. This library allows the user to treat individual components of molecules as C++ objects, and provides various templated lists and vector classes for manipulating these objects. Other utilities, such as minimizers and integrators, are continually being added to the body of code. Performance is a key consideration; the performance of simple benchmarks is comparable to that of hand-coded Fortran.

[1]  G. Huber,et al.  Weighted-ensemble Brownian dynamics simulations for protein association reactions. , 1996, Biophysical journal.

[2]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[3]  Shoshana J. Wodak,et al.  Development and parametrization of continuum solvent models. I. Models based on the boundary element method , 1996 .

[4]  Adrian E. Roitberg,et al.  MOIL: A program for simulations of macromolecules , 1995 .

[5]  J. Andrew McCammon,et al.  Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation , 1993 .

[6]  Rich Hickey Callbacks in C++ using template functors , 1995 .

[7]  Jack Dongarra,et al.  MPI: The Complete Reference , 1996 .

[8]  Michael J. Holst,et al.  Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods , 1995, J. Comput. Chem..

[9]  J. Andrew McCammon,et al.  Application of Poisson—Boltzmann solvation forces to macromolecular simulations , 1997 .

[10]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[11]  L. R. Scott,et al.  Parallelizing molecular dynamics using spatial decomposition , 1994, Proceedings of IEEE Scalable High Performance Computing Conference.

[12]  Piotr Bala,et al.  Quantum-classical Molecular Dynamics and Its Computer Implementation , 1995, Comput. Chem..

[13]  S.R. Kohn,et al.  A Parallel Software Infrastructure for Structured Adaptive Mesh Methods , 1995, Proceedings of the IEEE/ACM SC95 Conference.

[14]  Arieh Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[15]  Michael L. Nelson,et al.  C++ Programmer's Guide to the Standard Template Library , 1995 .

[16]  Arch D. Robison,et al.  C++ gets faster for scientific computing , 1996 .

[17]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[18]  Christoph Dellago,et al.  Efficient transition path sampling: Application to Lennard-Jones cluster rearrangements , 1998 .

[19]  Todd L. Veldhuizen,et al.  Expression templates , 1996 .

[20]  J. Andrew McCammon,et al.  Weighted-ensemble simulated annealing: Faster optimization on hierarchical energy surfaces , 1997 .

[21]  James Martin,et al.  Object-oriented analysis and design , 1992 .