Combine umbrella sampling with integrated tempering method for efficient and accurate calculation of free energy changes of complex energy surface

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

(2013) Yoshiharu Mori et al.   PHYSICAL REVIEW E

Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein

(2012) Qiang Shao et al.   JOURNAL OF CHEMICAL PHYSICS

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2012) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

Temperature-Accelerated Sampling and Amplified Collective Motion with Adiabatic Reweighting to Obtain Canonical Distributions and Ensemble Averages

(2012) Yue Hu et al.   Journal of Chemical Theory and Computation

Robustness in Protein Folding Revealed by Thermodynamics Calculations

(2012) Qiang Shao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

(2012) Soohyung Park et al.   PHYSICAL REVIEW LETTERS

Order parameters for macromolecules: Application to multiscale simulation

(2011) A. Singharoy et al.   JOURNAL OF CHEMICAL PHYSICS

Structure change of β-hairpin induced by turn optimization: An enhanced sampling molecular dynamics simulation study

(2011) Qiang Shao et al.   JOURNAL OF CHEMICAL PHYSICS

The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation

(2011) Qiang Shao et al.   JOURNAL OF CHEMICAL PHYSICS

Combined Metadynamics and Umbrella Sampling Method for the Calculation of Ion Permeation Free Energy Profiles

(2011) Yong Zhang et al.   Journal of Chemical Theory and Computation

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

(2010) Halvor S. Hansen et al.   Journal of Chemical Theory and Computation

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

(2009) Jeremy Curuksu et al.   JOURNAL OF CHEMICAL PHYSICS

A selective integrated tempering method

(2009) Lijiang Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison between integrated and parallel tempering methods in enhanced sampling simulations

(2009) Lijiang Yang et al.   JOURNAL OF CHEMICAL PHYSICS

Multidimensional generalized-ensemble algorithms for complex systems

(2009) Ayori Mitsutake et al.   JOURNAL OF CHEMICAL PHYSICS

Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water

(2009) Halvor S. Hansen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering

(2009) Ayori Mitsutake et al.   PHYSICAL REVIEW E

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

(2008) Hao Hu et al.   Annual Review of Physical Chemistry

Thermodynamics and kinetics simulations of multi-time-scale processes for complex systems

(2008) Yi Qin Gao et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS

An integrate-over-temperature approach for enhanced sampling

(2008) Yi Qin Gao   JOURNAL OF CHEMICAL PHYSICS

Adaptive biasing force method for scalar and vector free energy calculations

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

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