Coarse-graining entropy, forces, and structures

A generalized mean field theory of coarse-graining

(2011) Vinod Krishna et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Synthesis and Electronic Structure Determination ofN-Alkyl-Substituted Bis(imino)pyridine Iron Imides Exhibiting Spin Crossover Behavior

(2011) Amanda C. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Generalized-Yvon-Born-Green Model of Toluene

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

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

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

Reference state for the generalized Yvon–Born–Green theory: Application for coarse-grained model of hydrophobic hydration

(2010) J. W. Mullinax et al.   JOURNAL OF CHEMICAL PHYSICS

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

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining

(2010) Lanyuan Lu et al.   Journal of Chemical Theory and Computation

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

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

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

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

(2010) Giulia Rossi et al.   Soft Matter

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

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

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

(2009) Teemu Murtola 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

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

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

Front cover

(2009)   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multiscale modeling of emergent materials: biological and soft matter

(2009) Teemu Murtola et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Generalized Yvon-Born-Green Theory for Molecular Systems

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

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

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

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

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

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