Search Results - "Hünenberger, Philippe H"

Multistate Method to Efficiently Account for Tautomerism and Protonation in Alchemical Free-Energy Calculations by Champion, Candide, Hünenberger, Philippe H., Riniker, Sereina

“…The majority of drug-like molecules contain at least one ionizable group, and many common drug scaffolds are subject to tautomeric equilibria. Thus, these…”
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Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization by Oliveira, Marina P., Hünenberger, Philippe H.

“…We recently introduced the CombiFF scheme [Oliveira et al., J. Chem. Theory Comput. 2020, 16, 7525], an approach for the automated refinement of force-field…”
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New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field by Reif, Maria M, Hünenberger, Philippe H, Oostenbrink, Chris

“…A GROMOS force-field parameter set 54A8 is developed, which is based on the latest 54A7 set [Schmid et al. Eur. Biophys. J. 2011, 40, 843–856] and involves a…”
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Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ‑Variations, λ‑Extrapolations, and Biasing by Hahn, David F, König, Gerhard, Hünenberger, Philippe H

“…Alchemical free energy calculations using conventional molecular dynamics and thermodynamic integration rely on simulations performed at fixed values of the…”
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The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface by Walker-Gibbons, Rowan, Kubincová, Alžbeta, Hünenberger, Philippe H., Krishnan, Madhavi

“…Molecular dynamics studies have demonstrated that molecular water at an interface, with either a gas or a solid, displays anisotropic orientational behavior in…”
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An Alternative to Conventional λ‑Intermediate States in Alchemical Free Energy Calculations: λ‑Enveloping Distribution Sampling by König, Gerhard, Glaser, Nina, Schroeder, Benjamin, Kubincová, Alžbeta, Hünenberger, Philippe H, Riniker, Sereina

“…Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate…”
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A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set by Horta, Bruno A. C, Merz, Pascal T, Fuchs, Patrick F. J, Dolenc, Jozica, Riniker, Sereina, Hünenberger, Philippe H

“…This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The…”
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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 by Rocklin, Gabriel J, Mobley, David L, Dill, Ken A, Hünenberger, Philippe H

“…The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the…”
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Efficient Alchemical Intermediate States in Free Energy Calculations Using λ‑Enveloping Distribution Sampling by König, Gerhard, Ries, Benjamin, Hünenberger, Philippe H, Riniker, Sereina

“…Alchemical free energy calculations generally require intermediate states along a coupling parameter λ to establish sufficient phase space overlap for…”
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Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity–Basity Scale Revisited by Reif, Maria M, Hünenberger, Philippe H

“…The asymmetric solvation of ions can be defined as the tendency of a solvent to preferentially solvate anions over cations or cations over anions, at identical…”
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Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies by Kashefolgheta, Sadra, Oliveira, Marina P, Rieder, Salomé R, Horta, Bruno A. C, Acree, William E, Hünenberger, Philippe H

“…Experimental solvation free energies are nowadays commonly included as target properties in the validation and sometimes even in the calibration of…”
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Alchemical Free-Energy Calculations by Multiple-Replica λ‑Dynamics: The Conveyor Belt Thermodynamic Integration Scheme by Hahn, David F, Hünenberger, Philippe H

“…A new method is proposed to calculate alchemical free-energy differences based on molecular dynamics (MD) simulations, called the conveyor belt thermodynamic…”
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Martini Coarse-Grained Force Field: Extension to Carbohydrates by López, Cesar A, Rzepiela, Andrzej J, de Vries, Alex H, Dijkhuizen, Lubbert, Hünenberger, Philippe H, Marrink, Siewert J

“…We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for…”
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reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers by Hansen, Halvor S, Hünenberger, Philippe H

“…This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate…”
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Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li+ Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations by Prasetyo, Niko, Hünenberger, Philippe H, Hofer, Thomas S

“…A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM…”
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Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules by Rieder, Salomé R., Ries, Benjamin, Schaller, Kay, Champion, Candide, Barros, Emilia P., Hünenberger, Philippe H., Riniker, Sereina

“…Free-energy differences between pairs of end-states can be estimated based on molecular dynamics (MD) simulations using standard pathway-dependent methods such…”
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Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field by Gonçalves, Yan M. H, Senac, Caroline, Fuchs, Patrick F. J, Hünenberger, Philippe H, Horta, Bruno A. C

“…The effect of different treatments of the nonbonded interactions in simulations employing the recently introduced GROMOS-compatible 2016H66 force field is…”
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A new GROMOS force field for hexopyranose-based carbohydrates by Lins, Roberto D., Hünenberger, Philippe H.

“…A new parameter set (referred to as 45A4) is developed for the explicit‐solvent simulation of hexopyranose‐based carbohydrates. This set is compatible with the…”
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Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes by Oliveira, Marina P, Andrey, Maurice, Rieder, Salomé R, Kern, Leyla, Hahn, David F, Riniker, Sereina, Horta, Bruno A. C, Hünenberger, Philippe H

“…Direct optimization against experimental condensed-phase properties concerning small organic molecules still represents the most reliable way to calibrate the…”
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The GROMOS software for biomolecular simulation: GROMOS05 by Christen, Markus, Hünenberger, Philippe H., Bakowies, Dirk, Baron, Riccardo, Bürgi, Roland, Geerke, Daan P., Heinz, Tim N., Kastenholz, Mika A., Kräutler, Vincent, Oostenbrink, Chris, Peter, Christine, Trzesniak, Daniel, van Gunsteren, Wilfred F.

“…We present the latest version of the Groningen Molecular Simulation program package, GROMOS05. It has been developed for the dynamical modelling of…”
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