A reference implementation of the adaptive resolution scheme in ESPResSo

We review the adaptive resolution scheme (AdResS) from a technical perspective and collect arguments from several years of research, which culminates into the implementation of AdResS into the open-source package ESPResSo. This flexible implementation allows us to repeat all previous AdResS simulations with one program. We test this reference implementation and resimulate some results of the well-studied tetrahedral fluid from various previous studies to show the functionality of the package.

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

[2]  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.

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

[4]  G. Voth Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .

[5]  Matej Praprotnik,et al.  Concurrent triple-scale simulation of molecular liquids. , 2008, The Journal of chemical physics.

[6]  D. Frenkel,et al.  Understanding molecular simulation : from algorithms to applications. 2nd ed. , 2002 .

[7]  Kurt Kremer,et al.  Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back , 2009 .

[8]  Matej Praprotnik,et al.  Adaptive resolution scheme for efficient hybrid atomistic-mesoscale molecular dynamics simulations of dense liquids. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  Matej Praprotnik,et al.  Adaptive resolution simulation of liquid water , 2007 .

[10]  Michele Parrinello,et al.  Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. , 2007, Journal of chemical theory and computation.

[11]  Matej Praprotnik,et al.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution. , 2008, Annual review of physical chemistry.

[12]  Matej Praprotnik,et al.  FAST TRACK COMMUNICATION: Fractional dimensions of phase space variables: a tool for varying the degrees of freedom of a system in a multiscale treatment , 2007 .

[13]  D. Nicholson,et al.  Monte Carlo grand canonical ensemble calculation in a gas-liquid transition region for 12-6 Argon , 1975 .

[14]  Matej Praprotnik,et al.  Coupling different levels of resolution in molecular simulations. , 2009, The Journal of chemical physics.

[15]  Matej Praprotnik,et al.  Modeling diffusive dynamics in adaptive resolution simulation of liquid water. , 2007, The Journal of chemical physics.

[16]  Hans-Jörg Limbach,et al.  ESPResSo - an extensible simulation package for research on soft matter systems , 2006, Comput. Phys. Commun..

[17]  L.Delle Site,et al.  Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme. , 2007, 0709.2579.

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

[19]  Matej Praprotnik,et al.  Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat. , 2007, Soft matter.

[20]  Matej Praprotnik,et al.  Adaptive molecular resolution via a continuous change of the phase space dimensionality. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[21]  Matej Praprotnik,et al.  A macromolecule in a solvent: adaptive resolution molecular dynamics simulation. , 2007, The Journal of chemical physics.

[22]  Tim N. Heinz,et al.  Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations , 2001 .

[23]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[24]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[25]  Gregory A Voth,et al.  Multiscale coarse graining of liquid-state systems. , 2005, The Journal of chemical physics.

[26]  Johannes Neugebauer,et al.  Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding. , 2005, The Journal of chemical physics.