ESPResSo - an extensible simulation package for research on soft matter systems

Abstract We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing ESPResSo was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of ESPResSo is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like P 3 M, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators; it offers the usage of constraints, masses and rotational degrees of freedom; it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl -script driven user interface makes ESPResSo platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep ESPResSo extensible for future enhancements and additions. ESPResSo is implemented as an open source project with the goal to stimulate researchers to contribute to the package.

[1]  Bernward A. F. Mann.  The swelling behaviour of polyelectrolyte networks , 2005 .

[2]  D. C. Rapaport,et al.  The Art of Molecular Dynamics Simulation , 1997 .

[3]  David A. Weitz,et al.  Soft Condensed Matter , 2003 .

[4]  Kurt Kremer,et al.  Rheology and Microscopic Topology of Entangled Polymeric Liquids , 2004, Science.

[5]  Christian Holm,et al.  Electrostatic effects in soft matter and biophysics , 2001 .

[6]  Michael Rubinstein,et al.  Nonaffine Deformation and Elasticity of Polymer Networks , 1997 .

[7]  A. Kolb,et al.  Optimized Constant Pressure Stochastic Dynamics , 1999 .

[8]  Ulli Wolff.  Monte Carlo errors with less errors , 2004 .

[9]  K. Kremer,et al.  Multiscale simulation in polymer science , 2002 .

[10]  Laxmikant V. Kalé,et al.  NAMD: a Parallel, Object-Oriented Molecular Dynamics Program , 1996, Int. J. High Perform. Comput. Appl..

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

[12]  C. Holm,et al.  Polyelectrolyte Bundles , 2003, cond-mat/0312576.

[13]  David Chandler,et al.  Ion imaging measurement of collision-induced rotational alignment in Ar-NO scattering , 2001 .

[14]  Axel Arnold,et al.  MMM2D: A fast and accurate summation method for electrostatic interactions in 2D slab geometries , 2002 .

[15]  H. C. Andersen,et al.  Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .

[16]  W Smith,et al.  DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.

[17]  M. Deserno,et al.  HOW TO MESH UP EWALD SUMS. II. AN ACCURATE ERROR ESTIMATE FOR THE PARTICLE-PARTICLE-PARTICLE-MESH ALGORITHM , 1998, cond-mat/9807100.

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

[19]  S. Duane,et al.  Hybrid Monte Carlo , 1987 .

[20]  B. Dünweg,et al.  Parallel excluded volume tempering for polymer melts. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[21]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[22]  Christian Holm,et al.  Estimate of the Cutoff Errors in the Ewald Summation for Dipolar Systems , 2001 .

[23]  Axel Arnold,et al.  Attraction and unbinding of like-charged rods , 2004 .

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

[25]  Laxmikant V. Kale,et al.  NAMD2: Greater Scalability for Parallel Molecular Dynamics , 1999 .

[26]  Kurt Kremer,et al.  Swelling of polyelectrolyte networks. , 2005, The Journal of chemical physics.

[27]  Kurt Kremer,et al.  Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[28]  D. J. Montgomery,et al.  The physics of rubber elasticity , 1949 .

[29]  Christian Holm,et al.  Electrophoretic mobility of a charged colloidal particle: a computer simulation study , 2004 .

[30]  Kurt Kremer,et al.  Simulation of polymer melts. I. Coarse‐graining procedure for polycarbonates , 1998 .

[31]  O. Farago.  “Water-free” computer model for fluid bilayer membranes , 2003, cond-mat/0304203.

[32]  M. Pütz,et al.  Optimization techniques for parallel molecular dynamics using domain decomposition , 1998 .

[33]  Igor Pasichnyk,et al.  Coulomb interactions via local dynamics: a molecular-dynamics algorithm , 2004 .

[34]  Kurt Kremer,et al.  The nature of flexible linear polyelectrolytes in salt free solution: A molecular dynamics study , 1995 .

[35]  Axel Arnold,et al.  MMM1D: a method for calculating electrostatic interactions in one-dimensional periodic geometries. , 2005, The Journal of chemical physics.

[36]  Christian Holm,et al.  How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .

[37]  Rolf Strebel,et al.  Pieces of software for the Coulombic m body problem , 1999 .

[38]  Axel Arnold,et al.  Computer simulations of charged systems in partially periodic geometries , 2004 .

[39]  Nicos Martys,et al.  Velocity Verlet algorithm for dissipative-particle-dynamics-based models of suspensions , 1999 .

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

[41]  Christian Holm,et al.  Efficient Methods for Long Range Interactions in Periodic Geometries Plus One Application , 2004 .

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

[43]  P. Ahlrichs,et al.  Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics , 1999, cond-mat/9905183.

[44]  Rochish Thaokar,et al.  Apparent persistence length renormalization of bent DNA. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[45]  C. Tanford.  Macromolecules , 1994, Nature.

[46]  Kurt Kremer,et al.  Scaling in polyelectrolyte networks , 2004 .

[47]  Thomas Soddemann,et al.  A generic computer model for amphiphilic systems , 2001 .

[48]  Jörg Rottler,et al.  Local molecular dynamics with coulombic interactions. , 2004, Physical review letters.

[49]  Patrick W. Fowler,et al.  A model for the geometries of Van der Waals complexes , 1985 .

[50]  John Lekner,et al.  Summation of Coulomb fields in computer-simulated disordered systems , 1991 .

[51]  Kurt Kremer,et al.  Computer Simulations of the “Hairy Rod” Model , 2005 .

[52]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[53]  Kurt Kremer,et al.  Vectorized link cell Fortran code for molecular dynamics simulations for a large number of particles , 1989 .

[54]  E. H ckel,et al.  Zur Theorie der Elektrolyte , 1924 .

[55]  Axel Arnold,et al.  Efficient methods to compute long-range interactions for soft matter systems , 2005 .

[56]  Christian Holm,et al.  How to Mesh up Ewald Sums , 2000 .

[57]  Ralf Everaers,et al.  Constrained fluctuation theories of rubber elasticity: General results and an exactly solvable model , 1998 .

[58]  A. C. Maggs,et al.  Local simulation algorithms for Coulomb interactions. , 2002 .

[59]  Axel Arnold,et al.  Electrostatics in Periodic Slab Geometries I , 2002 .

[60]  Anders Ynnerman,et al.  GISMOS: Graphics and Interactive Steering of MOlecular Simulations , 2000 .

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

[62]  Kurt Kremer,et al.  Simulation of Polymer Melts. II. From Coarse-Grained Models Back to Atomistic Description , 1998 .

[63]  E. R. Smith.  Electrostatic energy in ionic crystals , 1981, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[64]  Vladimir Lobaskin,et al.  A new model for simulating colloidal dynamics , 2004 .

[65]  F Müller-Plathe,et al.  Reversing the perturbation in nonequilibrium molecular dynamics: an easy way to calculate the shear viscosity of fluids. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[66]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[67]  P. Español,et al.  Statistical Mechanics of Dissipative Particle Dynamics. , 1995 .

[68]  Lennart Nilsson,et al.  Advances in biomolecular simulations: methodology and recent applications , 2003, Quarterly Reviews of Biophysics.

[69]  Axel Arnold,et al.  A novel method for calculating electrostatic interactions in 2D periodic slab geometries , 2002 .

[70]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[71]  Kurt Kremer,et al.  Identifying the primitive path mesh in entangled polymer liquids , 2004 .

[72]  K. Kremer,et al.  Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[73]  J. Davenport.  Editor , 1960 .

[74]  G. Grest,et al.  Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation , 1990 .

[75]  A C Maggs,et al.  Local simulation algorithms for Coulombic interactions , 2002, Physical review letters.

[76]  Burkhard Dünweg,et al.  Lattice Boltzmann Simulation of Polymer-Solvent Systems , 1998 .

[77]  Axel Arnold,et al.  Electrostatics in periodic slab geometries. II , 2002 .

[78]  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 .