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

A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

(2012) Scott P. Carmichael et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Smoothing Protein Energy Landscapes by Integrating Folding Models with Structure Prediction

(2011) Ari Pritchard-Bell et al.   BIOPHYSICAL JOURNAL

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

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

On the Use of Stochastic Hessian Information in Optimization Methods for Machine Learning

(2011) Richard H. Byrd et al.   SIAM JOURNAL ON OPTIMIZATION

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

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