List of works - Philippe H Hünenberger

A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol

scientific article published on 08 August 2012

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

scientific article

A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions

scientific article

A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations.

scientific article published in August 2006

A 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

scientific article published on 10 November 2010

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

scientific article published on 01 June 2018

Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme

scientific article published on 25 March 2019

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

scientific article

An improved nucleic acid parameter set for the GROMOS force field

Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries

scientific article published on 26 August 2010

Biomolecular modeling: Goals, problems, perspectives

scientific article published on June 2006

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

scientific article

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

scientific article published on 19 July 2012

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry

Car-Parrinello Molecular Dynamics Simulations of CaCl2 Aqueous Solutions.

scientific article published on May 2008

Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations

scientific article published on 01 July 2005

Communication: estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.

scientific article published in November 2014

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

scientific article published on 01 June 2001

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

scientific article published in March 2006

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation

scientific article published in June 2006

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvat

scientific article published in April 2011

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water ⬇️

scientific article published on April 14, 2011

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

scientific article published on 01 August 2006

Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field

scientific article published on 18 May 2007

Conformational and dynamical properties of disaccharides in water: a molecular dynamics study

scientific article

Determinants of ligand binding to cAMP-dependent protein kinase.

scientific article published on February 1999

Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum-electrostatics study.

scientific article published in March 2006

Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: in quest of the biphasic effect

scientific article published on 07 November 2014

Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations

scientific article

Effect of trehalose on a phospholipid membrane under mechanical stress.

scientific article published on 3 July 2008

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling

scientific article published on 06 September 2021

Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients

scientific article published on 21 February 2013

Enantiomeric Segregation in the Gel Phase of Lipid Bilayers ⬇️

scientific article published on May 16, 2011

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

scientific article published in September 2010

Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies

scientific article published on 04 November 2020

Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions

scientific article published in 1996

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

scientific article published in June 2009

Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field

scientific article published on 27 February 2019

Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: a comparative molecular dynamics study

scientific article published in August 2006

Interfacial solvation can explain attraction between like-charged objects in aqueous solution

scientific article published on 01 March 2020

Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers

scientific article published on 10 May 2013

Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical Free-Energy Changes via λ-Dynamics: The λ-LEUS Scheme

scientific article published in August 2014

Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation

scientific article published on 08 November 2014

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

scientific article

Measuring 1H-1H and 1H-13C RDCs in methyl groups: example of pulse sequences with numerically optimized coherence transfer schemes

scientific article published on 01 January 2005

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

scientific article published on October 2003

Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells

scientific article published on 01 August 2002

Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions

scientific article published in March 2009

Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.

scientific article

Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection

Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): method and application to the complexation of cations by crown ethers.

scientific article published in June 2015

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

scientific article published on 24 May 2012

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

scientific article published on 25 March 2011

New functionalities in the GROMOS biomolecular simulation software

scientific article published on 11 November 2011

On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.

scientific article published in April 2015

On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution

scientific article published on 14 July 2007

Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited.

scientific article

Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS.

scientific article published on 7 July 2015

Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing

scientific article published on 27 February 2020

Phase-transition properties of glycerol-dipalmitate lipid bilayers investigated using molecular dynamics simulation

scientific article published on 05 May 2015

Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces

scientific article published on 02 November 2011

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol

scientific article

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules

scientific article published in 2022

Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: a molecular dynamics study

scientific article published on 21 March 2010

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology

scientific article published on 22 March 2022

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

scientific article published on 03 November 2015

Simulating Bilayers of Nonionic Surfactants with the GROMOS-Compatible 2016H66 Force Field

scientific article published on 23 August 2017

Simulating the Transition between Gel and Liquid-Crystal Phases of Lipid Bilayers: Dependence of the Transition Temperature on the Hydration Level

scientific article published on 01 August 2010

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

scientific article published on 24 November 2020

Temperature Dependence of the Dielectric Permittivity of Acetic Acid, Propionic Acid and Their Methyl Esters: A Molecular Dynamics Simulation Study

article

The Conveyor Belt Umbrella Sampling (CBUS) Scheme: Principle and Application to the Calculation of the Absolute Binding Free Energies of Alkali Cations to Crown Ethers

scientific article published on 25 March 2020

The GROMOS software for biomolecular simulation: GROMOS05.

scientific article

The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface

scientific article published in 2022

The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.

scientific article published in October 2006

Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex

scientific article published on 01 June 2010

Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water.

scientific article

Wilfred van Gunsteren: 35 Years of Biomolecular Simulation

scientific article published on 01 October 2012

List of works by Philippe H Hünenberger

A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.

A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions

A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations.

A 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

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

An improved nucleic acid parameter set for the GROMOS force field

Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries

Biomolecular modeling: Goals, problems, perspectives

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

Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

Car-Parrinello Molecular Dynamics Simulations of CaCl2 Aqueous Solutions.

Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations

Communication: estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation

Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvat

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water ⬇️

Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations

Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field

Conformational and dynamical properties of disaccharides in water: a molecular dynamics study

Determinants of ligand binding to cAMP-dependent protein kinase.

Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum-electrostatics study.

Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: in quest of the biphasic effect

Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations

Effect of trehalose on a phospholipid membrane under mechanical stress.

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling

Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients

Enantiomeric Segregation in the Gel Phase of Lipid Bilayers ⬇️

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling

Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies

Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions

In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.

Influence of the Treatment of Nonbonded Interactions on the Thermodynamic and Transport Properties of Pure Liquids Calculated Using the 2016H66 Force Field

Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: a comparative molecular dynamics study

Interfacial solvation can explain attraction between like-charged objects in aqueous solution

Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers

Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical Free-Energy Changes via λ-Dynamics: The λ-LEUS Scheme

Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation

Martini Coarse-Grained Force Field: Extension to Carbohydrates.

Measuring 1H-1H and 1H-13C RDCs in methyl groups: example of pulse sequences with numerically optimized coherence transfer schemes

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions

Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells

Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions

Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.

Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection

Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): method and application to the complexation of cations by crown ethers.

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters

New functionalities in the GROMOS biomolecular simulation software

On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.

On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution

Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited.

Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS.

Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing

Phase-transition properties of glycerol-dipalmitate lipid bilayers investigated using molecular dynamics simulation

Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces

Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol

Replica-Exchange Enveloping Distribution Sampling Using Generalized AMBER Force-Field Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules

Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: a molecular dynamics study

RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology

Revision of the GROMOS 56A6(CARBO) force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

Simulating Bilayers of Nonionic Surfactants with the GROMOS-Compatible 2016H66 Force Field

Simulating the Transition between Gel and Liquid-Crystal Phases of Lipid Bilayers: Dependence of the Transition Temperature on the Hydration Level

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

Temperature Dependence of the Dielectric Permittivity of Acetic Acid, Propionic Acid and Their Methyl Esters: A Molecular Dynamics Simulation Study

The Conveyor Belt Umbrella Sampling (CBUS) Scheme: Principle and Application to the Calculation of the Absolute Binding Free Energies of Alkali Cations to Crown Ethers

The GROMOS software for biomolecular simulation: GROMOS05.

The Role of Surface Chemistry in the Orientational Behavior of Water at an Interface

The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.

Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex

Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water.

Wilfred van Gunsteren: 35 Years of Biomolecular Simulation