Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations

Integral equation theory based direct and accelerated systematic coarse-graining approaches

(2018) S. Y. Mashayak et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Force Field for Imidazolium-Based Ionic Liquids

(2018) Alireza Moradzadeh et al.   Journal of Chemical Theory and Computation

Understanding three-body contributions to coarse-grained force fields

(2018) Christoph Scherer et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations

(2018) Gregor Deichmann et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics

(2018) Tristan Bereau et al.   PHYSICAL REVIEW LETTERS

BOCS: Bottom-up Open-source Coarse-graining Software

(2017) Nicholas J. H. Dunn et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Comparison of iterative inverse coarse-graining methods

(2016) David Rosenberger et al.   European Physical Journal-Special Topics

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

(2016) Nicholas J. H. Dunn et al.   JOURNAL OF CHEMICAL PHYSICS

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 glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

(2015) Michael Langeloth 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

Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA

(2015) S. Y. Mashayak et al.   PLoS One

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

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

Nuclear Quantum Effects in Water: A Multiscale Study

(2014) Sebastian Fritsch et al.   Journal of Chemical Theory and Computation

Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization

(2014) Jibao Lu et al.   Journal of Chemical Theory and Computation

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

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

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

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

A stochastic optimization approach to coarse-graining using a relative-entropy framework

(2013) Ilias Bilionis et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

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

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

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

Structure-based coarse-graining in liquid slabs

(2012) Mara Jochum et al.   JOURNAL OF CHEMICAL PHYSICS

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

(2012) Avisek Das 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

Coarse-grained molecular models of water: a review

(2012) Kevin R. Hadley et al.   MOLECULAR SIMULATION

Coarse-graining entropy, forces, and structures

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

Generalized-Yvon-Born-Green Model of Toluene

(2011) Christopher R. Ellis et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Coarse-Grained Computer Simulation of Nanoconfined Polyamide-6,6

(2011) Hossein Eslami et al.   MACROMOLECULES

Systematic Coarse Graining of 4-Cyano-4′-pentylbiphenyl

(2010) Grigorios Megariotis et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

(2010) Luca Larini et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Chemically accurate coarse graining of double-stranded DNA

(2010) A. Savelyev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

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

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

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

Inversion of radial distribution functions to pair forces by solving the Yvon–Born–Green equation iteratively

(2009) Hyung Min Cho et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer

(2009) Teemu Murtola 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

Generalized Yvon-Born-Green Theory for Molecular Systems

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

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

(2008) W. G. Noid 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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Water Modeled As an Intermediate Element between Carbon and Silicon†

(2008) Valeria Molinero et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2008) Hu-Jun Qian et al.   MACROMOLECULES

Correspondence between phase diagrams of the TIP5P water model and a spherically symmetric repulsive ramp potential with two characteristic length scales

(2008) Zhenyu Yan et al.   PHYSICAL REVIEW E

Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal

(2008) Christine Peter et al.   Soft Matter