Force-momentum-based self-guided Langevin dynamics: A rapid sampling method that approaches the canonical ensemble

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

(2011) Xiongwu Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Characterizing the denatured state of human prion 121–230

(2010) Cheng-I Lee et al.   BIOPHYSICAL CHEMISTRY

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

(2010) Michael S. Lee et al.   Journal of Chemical Theory and Computation

Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Translocation

(2010) Pushkar Y. Pendse et al.   JOURNAL OF MOLECULAR BIOLOGY

Interaction of an ionic complementary peptide with a hydrophobic graphite surface

(2010) Yuebiao Sheng et al.   PROTEIN SCIENCE

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

A computational modeling and molecular dynamics study of the Michaelis complex of human protein Z-dependent protease inhibitor (ZPI) and factor Xa (FXa)

(2009) Vasudevan Chandrasekaran et al.   JOURNAL OF MOLECULAR MODELING

Adsorption of an Ionic Complementary Peptide on the Hydrophobic Graphite Surface

(2009) Yuebiao Sheng et al.   Journal of Physical Chemistry C

Phase transformation of Cu precipitate in Fe–Cu alloy studied using self-guided molecular dynamics

(2009) Y. Abe et al.   PHILOSOPHICAL MAGAZINE LETTERS

Self-guided Langevin dynamics study of regulatory interactions in NtrC

(2009) Ana Damjanović et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Backbone Relaxation Coupled to the Ionization of Internal Groups in Proteins: A Self-Guided Langevin Dynamics Study

(2008) Ana Damjanović et al.   BIOPHYSICAL JOURNAL

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

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