A general purpose parallel molecular dynamics simulation program

We present a general purpose parallel molecular dynamics simulation code. The code can handle NVE, NVT, and NPT ensemble molecular dynamics, Langevin dynamics, and dissipative particle dynamics. Long-range interactions are handled by using the smooth particle mesh Ewald method. The implicit solvent model using solvent-accessible surface area was also implemented. Benchmark results using molecular dynamics, Langevin dynamics, and dissipative particle dynamics are given.

[1]  M. Karplus,et al.  Simulation of activation free energies in molecular systems , 1996 .

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

[3]  Alexander D. MacKerell,et al.  An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids , 2000 .

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

[5]  Nhan Phan-Thien,et al.  Microchannel flow of a macromolecular suspension , 2003 .

[6]  C. Lowe,et al.  An alternative approach to dissipative particle dynamics , 1999 .

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

[8]  Takao Yamazaki,et al.  A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers [Comput. Phys. Commun. 83 (1994) 1–13] , 1995 .

[9]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[10]  Bruce Hendrickson,et al.  A new parallel method for molecular dynamics simulation of macromolecular systems , 1996 .

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

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

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

[14]  Grant S. Heffelfinger,et al.  Parallel atomistic simulations , 2000 .

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

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

[17]  P. B. Warren,et al.  DISSIPATIVE PARTICLE DYNAMICS : BRIDGING THE GAP BETWEEN ATOMISTIC AND MESOSCOPIC SIMULATION , 1997 .

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

[19]  J. Apostolakis,et al.  Evaluation of a fast implicit solvent model for molecular dynamics simulations , 2002, Proteins.

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

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

[22]  G. Ciccotti,et al.  Algorithms for Brownian dynamics , 2003 .

[23]  R. C. Reeder,et al.  A Coarse Grain Model for Phospholipid Simulations , 2001 .