Coarse-graining errors and numerical optimization using a relative entropy framework.

The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise "first-principles") ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, S(rel), that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.

[1]  C. Jarzynski Nonequilibrium Equality for Free Energy Differences , 1996, cond-mat/9610209.

[2]  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.

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

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

[5]  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.

[6]  Alan K. Soper,et al.  Empirical potential Monte Carlo simulation of fluid structure , 1996 .

[7]  Margaret E. Johnson,et al.  Assessing thermodynamic-dynamic relationships for waterlike liquids. , 2009, The Journal of chemical physics.

[8]  M Scott Shell,et al.  Relative entropy as a universal metric for multiscale errors. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[9]  William George Noid,et al.  Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .

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

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

[12]  R. L. McGreevy,et al.  Reverse Monte Carlo Simulation: A New Technique for the Determination of Disordered Structures , 1988 .

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

[14]  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.

[15]  Tamar Schlick,et al.  New Algorithms for Macromolecular Simulation , 2006 .

[16]  William George Noid,et al.  A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials† , 2010 .

[17]  B. Brooks,et al.  Multiscale methods for macromolecular simulations. , 2008, Current opinion in structural biology.

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

[19]  Juan J. de Pablo,et al.  Molecular and multiscale modeling in chemical engineering – current view and future perspectives , 2005 .

[20]  Ilpo Vattulainen,et al.  Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. , 2009, The Journal of chemical physics.

[21]  M Scott Shell,et al.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems. , 2008, The Journal of chemical physics.

[22]  A. Pohorille,et al.  Free energy calculations : theory and applications in chemistry and biology , 2007 .

[23]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[24]  M. Wall,et al.  Allostery in a coarse-grained model of protein dynamics. , 2005, Physical review letters.

[25]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[26]  Alexander Lyubartsev,et al.  Systematic coarse-graining of molecular models by the Newton inversion method. , 2010, Faraday discussions.

[27]  Eric F Darve Numerical Methods for Calculating the Potential of Mean Force , 2006 .

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

[29]  F. Cilloco,et al.  Information-theory-based solution of the inverse problem in classical statistical mechanics. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

[31]  M Scott Shell,et al.  Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy. , 2009, Physical chemistry chemical physics : PCCP.

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

[33]  R. A. Leibler,et al.  On Information and Sufficiency , 1951 .

[34]  Reinier L. C. Akkermans,et al.  A structure-based coarse-grained model for polymer melts , 2001 .

[35]  T. L. Hill,et al.  An Introduction to Statistical Thermodynamics , 1960 .

[36]  J. Kirkwood Statistical Mechanics of Fluid Mixtures , 1935 .

[37]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

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