Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained levels of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, and the other containing only one-particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The hybrid and the atomistically resolved systems have the same statistical properties at the same physical conditions.

[1]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[2]  A. Narten,et al.  X-ray diffraction study and models of liquid methane at 92 K , 1981 .

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

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

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

[6]  Burkhard Dünweg,et al.  BROWNIAN DYNAMICS SIMULATIONS WITHOUT GAUSSIAN RANDOM NUMBERS , 1991 .

[7]  F. Schwabl,et al.  Quantum Mechanics , 1992 .

[8]  M. Cross,et al.  A multi-scale atomistic-continuum modelling of crack propagation in a two-dimensional macroscopic plate , 1998 .

[9]  Leonid V. Zhigilei,et al.  A combined molecular dynamics and finite element method technique applied to laser induced pressure wave propagation , 1999 .

[10]  Benedict Leimkuhler,et al.  Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.

[11]  J. Q. Broughton,et al.  Concurrent coupling of length scales: Methodology and application , 1999 .

[12]  Carlos E. Padilla,et al.  MBO(N)D: A multibody method for long‐time molecular dynamics simulations , 2000 .

[13]  W. Cai,et al.  Minimizing boundary reflections in coupled-domain simulations. , 2000, Physical review letters.

[14]  A. Malevanets,et al.  Solute molecular dynamics in a mesoscale solvent , 2000 .

[15]  Kurt Kremer,et al.  Multiscale Problems in Polymer Science: Simulation Approaches , 2001 .

[16]  Alessandro Laio,et al.  A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations , 2002 .

[17]  I. Snook,et al.  How hard is a colloidal "hard-sphere" interaction? , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[18]  A. Louis.  Beware of density dependent pair potentials , 2002, cond-mat/0205110.

[19]  Stefano Curtarolo,et al.  Dynamics of an inhomogeneously coarse grained multiscale system. , 2002, Physical review letters.

[20]  L Delle Site,et al.  Polymers near metal surfaces: selective adsorption and global conformations. , 2002, Physical review letters.

[21]  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.

[22]  Jack L. Skinner,et al.  Flexible TIP4P model for molecular dynamics simulation of liquid water , 2003 .

[23]  Kurt Kremer,et al.  Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[24]  Berend Smit,et al.  Phase Behavior and Induced Interdigitation in Bilayers Studied with Dissipative Particle Dynamics , 2003 .

[25]  Dirk Reith,et al.  Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..

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

[27]  Kurt Kremer,et al.  BPA-PC on a Ni111 surface: the interplay between adsorption energy and conformational entropy for different chain-end modifications. , 2004, Journal of the American Chemical Society.

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

[29]  Sabine H. L. Klapp,et al.  Why are effective potentials 'soft'? , 2004 .

[30]  M C Payne,et al.  "Learn on the fly": a hybrid classical and quantum-mechanical molecular dynamics simulation. , 2004, Physical review letters.

[31]  G. Voth,et al.  A new perspective on the coarse-grained dynamics of fluids. , 2004, The Journal of chemical physics.

[32]  Sabine Attinger,et al.  Multiscale Modelling and Simulation , 2004 .

[33]  Dusanka Janezic,et al.  Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation Study , 2004 .

[34]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[35]  Michael L. Klein,et al.  Coarse grain models and the computer simulation of soft materials , 2004 .

[36]  M. Tuckerman,et al.  Long time molecular dynamics for enhanced conformational sampling in biomolecular systems. , 2004, Physical review letters.

[37]  K. Schulten,et al.  Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Kurt Kremer,et al.  Adhesion of Polycarbonate Blends on a Nickel Surface , 2005 .

[39]  D. Janežič,et al.  Molecular dynamics integration and molecular vibrational theory. III. The infrared spectrum of water. , 2005, The Journal of chemical physics.

[40]  Dusanka Janezic,et al.  Molecular dynamics integration and molecular vibrational theory. II. Simulation of nonlinear molecules. , 2005, The Journal of chemical physics.

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

[42]  Gregory A Voth,et al.  Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations. , 2005, The Journal of chemical physics.

[43]  Dusanka Janezic,et al.  Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators. , 2005, The Journal of chemical physics.