Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

A variational approach to nucleation simulation

(2016) Pablo M. Piaggi et al.   FARADAY DISCUSSIONS

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling

(2016) Patrick Shaffer et al.   Journal of Chemical Theory and Computation

Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling

(2016) James McCarty et al.   Journal of Chemical Theory and Computation

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

(2016) Patrick Shaffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A variational approach to nucleation simulation

(2016) Pablo M. Piaggi et al.   FARADAY DISCUSSIONS

Well-Tempered Variational Approach to Enhanced Sampling

(2015) Omar Valsson et al.   Journal of Chemical Theory and Computation

Variationally Optimized Free-Energy Flooding for Rate Calculation

(2015) James McCarty et al.   PHYSICAL REVIEW LETTERS

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

Applications of the Cross-Entropy Method to Importance Sampling and Optimal Control of Diffusions

(2014) Wei Zhang et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Coarse-Graining Methods for Computational Biology

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

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Beyond the Van Der Waals loop: What can be learned from simulating Lennard-Jones fluids inside the region of phase coexistence

(2012) Kurt Binder et al.   AMERICAN JOURNAL OF PHYSICS

Free energy computations by minimization of Kullback–Leibler divergence: An efficient adaptive biasing potential method for sparse representations

(2012) I. Bilionis et al.   JOURNAL OF COMPUTATIONAL PHYSICS

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

(2011) Aviel Chaimovich 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