Using collective variables to drive molecular dynamics simulations

Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering

(2012) Lianqing Zheng et al.   Journal of Chemical Theory and Computation

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics

(2010) C. F. Abrams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain

(2010) G. Brannigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling

(2009) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements

(2009) Davide Alemani et al.   Journal of Chemical Theory and Computation

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories

(2008) Deniz Sezer et al.   JOURNAL OF CHEMICAL PHYSICS

Adaptive biasing force method for scalar and vector free energy calculations

(2008) Eric Darve et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics of Surface-Moving Thermally Driven Nanocars

(2008) Alexei V. Akimov et al.   Journal of Chemical Theory and Computation

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Asynchronous replica exchange for molecular simulations

(2007) Emilio Gallicchio et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY