Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures

A generalized-Yvon-Born-Green method for coarse-grained modeling

(2015) J. F. Rudzinski et al.   European Physical Journal-Special Topics

Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

(2015) Nicholas J. H. Dunn et al.   JOURNAL OF CHEMICAL PHYSICS

The impact of resolution upon entropy and information in coarse-grained models

(2015) Thomas T. Foley et al.   JOURNAL OF CHEMICAL PHYSICS

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions

(2015) Joseph F. Rudzinski et al.   Journal of Chemical Theory and Computation

Transferability and Nonbond Functional Form of Coarse Grained Force Field – Tested on Linear Alkanes

(2015) Fenglei Cao et al.   Journal of Chemical Theory and Computation

Thermomechanically Consistent and Temperature Transferable Coarse-Graining of Atactic Polystyrene

(2015) David D. Hsu et al.   MACROMOLECULES

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale

(2014) J. McCarty et al.   JOURNAL OF CHEMICAL PHYSICS

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

(2014) Timothy C. Moore et al.   JOURNAL OF CHEMICAL PHYSICS

Transferability of Coarse-Grained Force Field for nCB Liquid Crystal Systems

(2014) Jianguo Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method

(2014) Joseph F. Rudzinski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hidden Scale Invariance in Condensed Matter

(2014) Jeppe C. Dyre   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

(2013) Cahit Dalgicdir et al.   JOURNAL OF CHEMICAL PHYSICS

Fitting coarse-grained distribution functions through an iterative force-matching method

(2013) Lanyuan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Predicting the thermodynamics by using state-dependent interactions

(2013) Giuseppe D'Adamo et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

A pH-dependent coarse-grained model for peptides

(2013) Marta Enciso et al.   Soft Matter

Scaling behavior and local structure of ion aggregates in single-ion conductors

(2013) Keran Lu et al.   Soft Matter

A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

(2012) Chia-Chun Fu et al.   JOURNAL OF CHEMICAL PHYSICS

The Role of Many-Body Correlations in Determining Potentials for Coarse-Grained Models of Equilibrium Structure

(2012) Joseph F. Rudzinski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamic Consistency between Analytic Integral Equation Theory and Coarse-Grained Molecular Dynamics Simulations of Homopolymer Melts

(2012) J. McCarty et al.   MACROMOLECULES

Thermodynamic transferability of coarse-grained potentials for polymer–additive systems

(2012) Emiliano Brini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On developing coarse-grained models for biomolecular simulation: a review

(2012) Sereina Riniker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Thermodynamic Consistency in Variable-Level Coarse Graining of Polymeric Liquids

(2012) A. J. Clark et al.   PHYSICAL REVIEW LETTERS

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

Coarse-graining entropy, forces, and structures

(2011) Joseph F. Rudzinski et al.   JOURNAL OF CHEMICAL PHYSICS

Towards an understanding of many-particle effects in hydrophobic association in methane solutions

(2011) Sergei Izvekov   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials

(2011) Lanyuan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

(2011) Carl Caleman et al.   Journal of Chemical Theory and Computation

Exploration of Transferability in Multiscale Coarse-Grained Peptide Models

(2011) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transferable Potentials for Phase Equilibria−Coarse-Grain Description for Linear Alkanes

(2011) Katie A. Maerzke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Conditional reversible work method for molecular coarse graining applications

(2011) Emiliano Brini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2010) Sergei Izvekov et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

(2010) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

Temperature dependence of coarse-grained potentials for liquid hexane

(2010) Karim Farah et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Recovering physical potentials from a model protein databank

(2010) J. W. Mullinax et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Coarse-Graining of the Protein Energy Landscape

(2010) Ronald D. Hills et al.   PLoS Computational Biology

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

(2009) Han Wang et al.   EUROPEAN PHYSICAL JOURNAL E

Multiscale simulation of soft matter systems

(2009) Christine Peter et al.   FARADAY DISCUSSIONS

Systematic coarse-graining of molecular models by the Newton inversion method

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

Pressure-energy correlations in liquids. III. Statistical mechanics and thermodynamics of liquids with hidden scale invariance

(2009) Thomas B. Schrøder et al.   JOURNAL OF CHEMICAL PHYSICS

Pressure-energy correlations in liquids. IV. “Isomorphs” in liquid phase diagrams

(2009) Nicoletta Gnan et al.   JOURNAL OF CHEMICAL PHYSICS

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

(2009) Marcos R. Betancourt et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains

(2009) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

(2009) Vinod Krishna et al.   JOURNAL OF CHEMICAL PHYSICS

Extended ensemble approach for deriving transferable coarse-grained potentials

(2009) J. W. Mullinax et al.   JOURNAL OF CHEMICAL PHYSICS

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

(2009) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials

(2009) J. W. Mullinax et al.   Journal of Physical Chemistry C

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy

(2009) Aviel Chaimovich et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effective force coarse-graining

(2009) Yanting Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Generalized Yvon-Born-Green Theory for Molecular Systems

(2009) J. W. Mullinax et al.   PHYSICAL REVIEW LETTERS

A Bayesian statistics approach to multiscale coarse graining

(2008) Pu Liu et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: The case of carbon dioxide

(2008) B. M. Mognetti et al.   JOURNAL OF CHEMICAL PHYSICS

A novel algorithm for creating coarse-grained, density dependent implicit solvent models

(2008) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

Temperature-Transferable Coarse-Grained Potentials for Ethylbenzene, Polystyrene, and Their Mixtures

(2008) Hu-Jun Qian et al.   MACROMOLECULES

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE