Development of a general purpose molecular simulation system from microscopic to mesoscopic scales

[1]  Takao Yamazaki,et al.  A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers , 1994 .

[2]  Piero Procacci,et al.  Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble , 1998 .

[3]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[4]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[5]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[6]  H. C. Andersen Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[7]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[8]  M. Parrinello,et al.  Crystal structure and pair potentials: A molecular-dynamics study , 1980 .

[9]  N. Karasawa,et al.  Acceleration of convergence for lattice sums , 1989 .

[10]  M. Tuckerman,et al.  Understanding Modern Molecular Dynamics: Techniques and Applications , 2000 .

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

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

[13]  A. T. Hagler,et al.  ENERGY FUNCTIONS FOR PEPTIDES AND PROTEINS PART 2, THE AMIDE HYDROGEN BOND AND CALCULATION OF AMIDE CRYSTAL PROPERTIES , 1974 .

[14]  David Brown,et al.  A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity. , 1997 .

[15]  Wolfgang J. Paul,et al.  A special purpose parallel computer for molecular dynamics: motivation, design, implementation, and application , 1987 .

[16]  Kwang Jin Oh,et al.  A parallel molecular dynamics simulation scheme for a molecular system with bond constraints in NPT ensemble , 2006, Comput. Phys. Commun..

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

[18]  J. Koelman,et al.  Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics , 1992 .