Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment

Enhancing QM/MM Molecular Dynamics Sampling in Explicit Environments via an Orthogonal-Space-Random-Walk-Based Strategy

(2011) Donghong Min et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optimization of partial multicanonical molecular dynamics simulations applied to an alaninedipeptide in explicit water solvent

(2010) Hisashi Okumura   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling

(2009) Lianqing Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

(2008) Lianqing Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals

(2008) Lianqing Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations

(2008) Lianqing Zheng 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