Best Practices in Constant pH MD Simulations: Accuracy and Sampling

Scalable Constant pH Molecular Dynamics in GROMACS

(2022) Noora Aho et al.   Journal of Chemical Theory and Computation

The accelerated weight histogram method for alchemical free energy calculations

(2021) M. Lundborg et al.   JOURNAL OF CHEMICAL PHYSICS

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

(2021) Anna Pavlova et al.   Journal of Physical Chemistry Letters

Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids

(2020) P. Buslaev et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

(2020) Gerrit Groenhof et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions

(2020) Oleksandr O. Sofronov et al.   Journal of Physical Chemistry Letters

GPCRmd uncovers the dynamics of the 3D-GPCRome

(2020) Ismael Rodríguez-Espigares et al.   NATURE METHODS

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

(2020) Szilárd Páll et al.   JOURNAL OF CHEMICAL PHYSICS

A pH Replica Exchange scheme in the Stochastic Titration constant-pH MD method

(2019) Diogo Vila-Viçosa et al.   Journal of Chemical Theory and Computation

Reservoir pH replica exchange

(2018) Ana Damjanovic et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Biophysical experiments and biomolecular simulations: A perfect match?

(2018) Sandro Bottaro et al.   SCIENCE

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer

(2016) Serena Donnini et al.   Journal of Chemical Theory and Computation

Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations

(2016) Pavel Buslaev et al.   Journal of Chemical Theory and Computation

Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations

(2016) Plamen Dobrev et al.   Journal of Chemical Theory and Computation

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

(2016) Yandong Huang et al.   Journal of Chemical Theory and Computation

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method

(2015) Yunjie Chen et al.   Journal of Chemical Theory and Computation

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Accelerated weight histogram method for exploring free energy landscapes

(2014) V. Lindahl et al.   JOURNAL OF CHEMICAL PHYSICS

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

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

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

Classical Electrostatics for Biomolecular Simulations

(2013) G. Andrés Cisneros et al.   CHEMICAL REVIEWS

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

(2013) Garrett B. Goh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

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

Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies

(2011) Jennifer L. Knight 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

The structural basis for agonist and partial agonist action on a β1-adrenergic receptor

(2011) Tony Warne et al.   NATURE

pH replica-exchange method based on discrete protonation states

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

Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

(2010) Yilin Meng et al.   Journal of Chemical Theory and Computation

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

(2010) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Error and efficiency of replica exchange molecular dynamics simulations

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

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY