The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials.

The ability of particle-based coarse-grain potentials, derived using the recently proposed multiscale coarse-graining (MS-CG) methodology [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] to reconstruct atomistic free-energy surfaces in coarse-grain coordinates is discussed. The MS-CG method is based on force-matching generalized forces associated with the coarse-grain coordinates. In this work, we show that the MS-CG method recovers only part of the atomistic free-energy landscape in the coarse-grain coordinates (termed the potential of mean force contribution). The portion of the atomistic free-energy landscape that is left out in the MS-CG procedure contributes to a pressure difference between atomistic and coarse-grain ensembles. Employing one- and two-site coarse-graining of nitromethane as worked examples, we discuss the virial and compressibility constraints to incorporate a pressure correction interaction into the MS-CG potentials and improve performance at different densities. The nature of the pressure correction interaction is elucidated and compared with those used in structure-based coarse-graining. As pairwise approximations to the atomistic free-energy, the MS-CG potentials naturally depend on the variables describing a thermodynamic state, such as temperature and density. Such dependencies limit state-point transferability. For nitromethane, the one- and two-site MS-CG potentials appear to be transferable across a broad range of temperatures. In particular, the two-site models, which are matched to low and ambient temperature liquid states, perform well in simulations of the ambient crystal structure. In contrast, the transferability of the MS-CG models of nitromethane across different densities is found to be problematic. To achieve better state-point transferability, density dependent MS-CG potentials are introduced and their performance is examined in simulations of nitromethane under various thermodynamic conditions, including shocked states.

[1]  Jim Pfaendtner,et al.  A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.

[2]  Jhih-Wei Chu,et al.  Emerging methods for multiscale simulation of biomolecular systems , 2007 .

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

[4]  C. Mader Numerical Modeling of Explosives and Propellants , 2007 .

[5]  Potential optimization for the calculation of shocked liquid nitromethane properties , 2007 .

[6]  Jijun Zhao,et al.  Compressibility of liquid nitromethane in the high-pressure regime , 2006 .

[7]  P G Bolhuis,et al.  Many-body interactions and correlations in coarse-grained descriptions of polymer solutions. , 2001, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

[9]  A. Delpuech,et al.  RAMAN SCATTERING TEMPERATURE MEASUREMENT BEHIND A SHOCK WAVE , 1984 .

[10]  Wataru Shinoda,et al.  Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .

[11]  Marina Guenza,et al.  Theoretical models for bridging timescales in polymer dynamics , 2008 .

[12]  S. P. Gill,et al.  Physics of Shock Waves and High-Temperature Hydrodynamic Phenomena , 2002 .

[13]  Margaret E. Johnson,et al.  Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.

[14]  Florian Müller-Plathe,et al.  Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains. , 2005, The journal of physical chemistry. B.

[15]  A. Lyubartsev,et al.  Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[16]  W. D. Otter,et al.  Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates , 2000 .

[17]  John G. Curro,et al.  Mapping of Explicit Atom onto United Atom Potentials , 1998 .

[18]  Gregory A Voth,et al.  Mixed Resolution Modeling of Interactions in Condensed-Phase Systems. , 2009, Journal of chemical theory and computation.

[19]  Michiel Sprik,et al.  Free energy from constrained molecular dynamics , 1998 .

[20]  Betsy M. Rice,et al.  Molecular dynamics study of the melting of nitromethane , 2003 .

[21]  David C. Schwartz,et al.  Effect of confinement on DNA dynamics in microfluidic devices , 2003 .

[22]  James B. Adams,et al.  Interatomic Potentials from First-Principles Calculations: The Force-Matching Method , 1993, cond-mat/9306054.

[23]  Weis,et al.  Iterative predictor-corrector method for extraction of the pair interaction from structural data for dense classical liquids. , 1986, Physical review. A, General physics.

[24]  Gregory A Voth,et al.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.

[25]  Alexander P. Lyubartsev,et al.  OSMOTIC AND ACTIVITY COEFFICIENTS FROM EFFECTIVE POTENTIALS FOR HYDRATED IONS , 1997 .

[26]  Betsy M. Rice,et al.  Molecular Dynamics Simulations of Normal Mode Vibrational Energy Transfer in Liquid Nitromethane , 2004 .

[27]  Michael L. Klein,et al.  A coarse grain model for n-alkanes parameterized from surface tension data , 2003 .

[28]  Marcus Müller,et al.  Simulations of theoretically informed coarse grain models of polymeric systems. , 2010, Faraday discussions.

[29]  Gregory A. Voth,et al.  Chapter 7 Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior , 2008 .

[30]  P. Nealey,et al.  Theoretically informed coarse grain simulations of block copolymer melts: method and applications , 2009 .

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

[32]  Alan K. Soper,et al.  The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa , 2000 .

[33]  Gregory A Voth,et al.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.

[34]  A. Violi,et al.  A Coarse-Grained Molecular Dynamics Study of Carbon Nanoparticle Aggregation. , 2006, Journal of chemical theory and computation.

[35]  Qiang Shi,et al.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. , 2006, The journal of physical chemistry. B.

[36]  Gregory C Rutledge,et al.  Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains. , 2009, The Journal of chemical physics.

[37]  Shekhar Garde,et al.  Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials. , 2005, The Journal of chemical physics.

[38]  Jijun Zhao,et al.  Structural and vibrational properties of solid nitromethane under high pressure by density functional theory. , 2006, The Journal of chemical physics.

[39]  F. L. Yarger,et al.  Compression of solid nitromethane to 15 GPa at 298 K , 1986 .

[40]  Wataru Shinoda,et al.  Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data. , 2010, The journal of physical chemistry. B.

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

[42]  S. Trevino,et al.  A study of methyl reorientation in solid nitromethane by neutron scattering , 1980 .

[43]  Avisek Das,et al.  The multiscale coarse-graining method. V. Isothermal-isobaric ensemble. , 2010, The Journal of chemical physics.

[44]  Jean-Pierre Hansen,et al.  VAN DER WAALS-LIKE INSTABILITY IN SUSPENSIONS OF MUTUALLY REPELLING CHARGED COLLOIDS , 1997 .

[45]  Erpenbeck Molecular dynamics of detonation. I. Equation of state and Hugoniot curve for a simple reactive fluid. , 1992, Physical Review A. Atomic, Molecular, and Optical Physics.

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

[47]  Florian Müller-Plathe,et al.  Transferability of coarse-grained force fields: the polymer case. , 2008, The Journal of chemical physics.

[48]  P. P. Ewald Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .

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

[50]  E. Bourasseau,et al.  Molecular based equation of state for shocked liquid nitromethane. , 2009, Journal of hazardous materials.

[51]  Frank L. H. Brown,et al.  Implicit solvent simulation models for biomembranes , 2005, European Biophysics Journal.

[52]  G. Ciccotti,et al.  Hoover NPT dynamics for systems varying in shape and size , 1993 .

[53]  Avisek Das,et al.  The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. , 2009, The Journal of chemical physics.

[54]  Roberto Car,et al.  Free energy profile along a discretized reaction path via the hyperplane constraint force and torque. , 2005, The Journal of chemical physics.

[55]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

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

[57]  Wataru Shinoda,et al.  Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. , 2010, The journal of physical chemistry. B.

[58]  Scott Brown,et al.  Coarse-grained sequences for protein folding and design , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[59]  Kurt Kremer,et al.  Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? , 2009, The European physical journal. E, Soft matter.

[60]  E. Bourasseau,et al.  Microscopic approaches to liquid nitromethane detonation properties. , 2008, The journal of physical chemistry. B.

[61]  Gregory A Voth,et al.  Multiscale coarse-graining of ionic liquids. , 2006, The journal of physical chemistry. B.

[62]  F. Stillinger,et al.  An orientational perturbation theory for pure liquid water , 1993 .

[63]  Gregory A Voth,et al.  Modeling real dynamics in the coarse-grained representation of condensed phase systems. , 2006, The Journal of chemical physics.

[64]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[65]  Gregory A Voth,et al.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. , 2008, The Journal of chemical physics.

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

[67]  Wataru Shinoda,et al.  A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. , 2009, Journal of chemical theory and computation.

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

[69]  Florian Müller-Plathe,et al.  Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[70]  Sergei Izvekov,et al.  The effect of temperature on nanoparticle clustering , 2007 .

[71]  B. Rice,et al.  Theoretical Studies of Solid Nitromethane , 2000 .

[72]  Alexander P. Lyubartsev,et al.  Multiscale modeling of lipids and lipid bilayers , 2005, European Biophysics Journal.

[73]  R. L. Henderson A uniqueness theorem for fluid pair correlation functions , 1974 .

[74]  Marcus Müller,et al.  Theoretically informed coarse grain simulations of polymeric systems. , 2009, The Journal of chemical physics.

[75]  D. Schiferl,et al.  The structure of nitromethane at pressures of 0.3 to 6.0 GPa , 1985 .

[76]  Kurt Kremer,et al.  Multiscale simulation of soft matter systems. , 2010, Faraday discussions.

[77]  F. Murnaghan The Compressibility of Media under Extreme Pressures. , 1944, Proceedings of the National Academy of Sciences of the United States of America.

[78]  Gregory A Voth,et al.  Multiscale coarse-graining of monosaccharides. , 2007, The journal of physical chemistry. B.

[79]  R. Larson,et al.  The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.

[80]  Betsy M. Rice,et al.  Molecular Dynamics Simulations of Liquid Nitromethane , 2001 .

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

[82]  K. Kremer,et al.  Aggregation and vesiculation of membrane proteins by curvature-mediated interactions , 2007, Nature.

[83]  Gregory A. Voth,et al.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.