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

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

STOCK: Structure mapper and online coarse-graining kit for molecular simulations

(2014) Staš Bevc et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Perspective: Coarse-grained models for biomolecular systems

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

MagiC: Software Package for Multiscale Modeling

(2013) Alexander Mirzoev et al.   Journal of Chemical Theory and Computation

Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining

(2013) Anu Nagarajan et al.   Journal of Chemical Theory and Computation

Thermodynamic state-dependent structure-based coarse-graining of confined water

(2012) S. Y. Mashayak et al.   JOURNAL OF CHEMICAL PHYSICS

Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions

(2012) Pritam Ganguly et al.   Journal of Chemical Theory and Computation

Structure Formation of Toluene around C60: Implementation of the Adaptive Resolution Scheme (AdResS) into GROMACS

(2012) Sebastian Fritsch et al.   Journal of Chemical Theory and Computation

Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

(2012) Olga Bezkorovaynaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

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

IBIsCO: A molecular dynamics simulation package for coarse-grained simulation

(2011) Hossein Ali Karimi-Varzaneh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane

(2011) Victor Rühle et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Multiscale modeling of soft matter: scaling of dynamics

(2011) Dominik Fritz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Coupling different levels of resolution in molecular simulations

(2010) Simón Poblete et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

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

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

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

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

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

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   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

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Water Modeled As an Intermediate Element between Carbon and Silicon†

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

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry