Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

Recent development and application of constant pH molecular dynamics

(2014) Wei Chen et al.   MOLECULAR SIMULATION

Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

pH-Dependent Dynamics of Complex RNA Macromolecules

(2013) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge

(2013) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids

(2013) Garrett B. Goh et al.   Journal of Physical Chemistry Letters

Self-Assembly and Bilayer–Micelle Transition of Fatty Acids Studied by Replica-Exchange Constant pH Molecular Dynamics

(2013) Brian H. Morrow et al.   LANGMUIR

Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

(2012) Brian H. Morrow et al.   JOURNAL OF CHEMICAL PHYSICS

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

(2012) Jason A. Wallace et al.   JOURNAL OF CHEMICAL PHYSICS

Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels

(2012) Jirasak Wong-ekkabut et al.   Journal of Chemical Theory and Computation

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

(2012) Stefano Piana et al.   PLoS One

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent

(2011) Garrett B. Goh et al.   Journal of Chemical Theory and Computation

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

(2011) Jason A. Wallace et al.   Journal of Chemical Theory and Computation

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

(2011) Yuhang Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulating pH Titration of a Single Surfactant in Ionic and Nonionic Surfactant Micelles

(2011) Brian H. Morrow et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

(2011) Evan J. Arthur et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

(2011) Jason A. Wallace et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

(2010) Sarah L. Williams et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

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

Molecular Dynamics Simulations of a Reversibly Folding β-Heptapeptide in Methanol: Influence of the Treatment of Long-Range Electrostatic Interactions

(2009) Maria M. Reif et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

(2008) Ilja V. Khavrutskii et al.   JOURNAL OF CHEMICAL PHYSICS