xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Multiple state transition interface sampling of alanine dipeptide in explicit solvent

(2011) Wei-Na Du et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

(2011) John D. Chodera et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Error and efficiency of simulated tempering simulations

(2010) Edina Rosta et al.   JOURNAL OF CHEMICAL PHYSICS

Exchange Often and Properly in Replica Exchange Molecular Dynamics

(2010) Daniel J. Sindhikara et al.   Journal of Chemical Theory and Computation

Error and efficiency of replica exchange molecular dynamics simulations

(2009) Edina Rosta et al.   JOURNAL OF CHEMICAL PHYSICS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Statistically optimal analysis of samples from multiple equilibrium states

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

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

(2008) Mark J. Abraham 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

Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach

(2008) Sanghyun Park   PHYSICAL REVIEW E