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A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditionsMartini Coarse-Grained Force Field: Extension to Carbohydrates.Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set.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.The GROMOS software for biomolecular simulation: GROMOS05.Conformational and dynamical properties of disaccharides in water: a molecular dynamics studyUsing 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.Biomolecular modeling: Goals, problems, perspectives.Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.Effect of trehalose on a phospholipid membrane under mechanical stress.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 effectsAn Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles.Calculation of Derivative Thermodynamic Hydration and Aqueous Partial Molar Properties of Ions Based on Atomistic Simulations.Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited.Car-Parrinello Molecular Dynamics Simulations of CaCl2 Aqueous Solutions.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.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.Determinants of ligand binding to cAMP-dependent protein kinase.Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: a molecular dynamics study.The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.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.Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations.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.Simulating Bilayers of Nonionic Surfactants with the GROMOS-Compatible 2016H66 Force Field.Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): method and application to the complexation of cations by crown ethers.On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.Communication: estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical Free-Energy Changes via λ-Dynamics: The λ-LEUS Scheme.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.Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.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 solvatComputation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions.In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum-electrostatics study.Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: a comparative molecular dynamics study.Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS.An improved nucleic acid parameter set for the GROMOS force field
P50
Q28269160-17827419-1FF1-49D2-BE99-FF104396E269Q30381806-E1DE3B2B-DB51-48BE-B103-7DD218F17C09Q31920192-FE65394F-1D3E-4B85-981F-52D20C865DABQ33468074-0553560A-74AE-495A-A5A5-70E53B10E8D6Q34287081-732CEA7F-4B17-4044-88F9-02E0FD3A1A8EQ34457783-D7D3DCAE-B570-4137-8827-478792288D26Q34646721-9B9DBEFD-C394-4190-BE5D-092AB3034087Q34978974-25346FB9-6A9E-4A55-A6A0-86E079613853Q36500277-4D26E80C-A274-44FD-AC32-998F6A0D31DDQ36631366-A37A183E-F851-4D8A-A037-13BC4DFC5B02Q36908321-F77607A2-31AB-4B81-8A98-55B21080BFDDQ37337108-26BE71A3-E41C-437F-85B9-5F0553DB03E2Q38647441-5CAD8F15-9CFA-446C-AF1E-FB4F2F0792F1Q39541617-47B9A8B0-CCB3-483F-A586-B54E12EB2C00Q39771269-C290C9D7-D1B0-4DF9-A753-1CF737C026C6Q40259408-B4DBD262-63C5-490B-B305-A0284830B911Q40276110-29A2C22C-C824-48F6-B887-7D8E4F5578D4Q40298316-E344376E-08BB-476E-BB9C-C6539222FA3CQ41608927-B3302E4E-8265-4942-BF25-2974887AEE86Q43122417-359E141B-8CEB-4D2F-97D6-72B653D51D1BQ43259843-3EE05556-1FE6-4CA4-8379-C2B3A6AEAF07Q45073969-4B5623F7-62E0-46FB-AF9A-3D536448A97EQ46848480-B439B0A8-E7CA-401A-A96A-7A6B039F1721Q47335402-CCAF2C33-4665-42E8-B739-B70F53A965F4Q47918089-AF659526-6F4E-45F2-9526-BCE461FD6C5FQ50694782-F0AB94D0-4F96-4158-9072-0ADB4AA389F4Q50737682-2520675F-1E86-4CBB-BCF8-A7E15732882EQ50768859-140D2C1B-3A74-48FE-969C-562125C429F7Q50788146-533DDE61-FF14-46A2-BA81-6CC6B600EC9FQ51037936-0A30A555-918E-4FB4-90BD-41184A523AB8Q51037946-DF0A046F-CCB9-49DE-98A2-8BA00485061EQ51578620-BAE4F1CC-6260-4FE0-9EA8-7EA24C8A992CQ51630155-1A33EB38-EB22-4010-8340-6EC4F838AAFCQ51630813-D9FD7B7C-A5D7-4A86-A03B-01BEDFCD3E57Q51812988-D3DC4283-5B5C-47CA-9138-AB18138C59A0Q51822734-3482B6D7-C29E-46BE-9931-E4EFEBCF4781Q51944480-322485E5-49C4-4E7B-9D5F-385033DCFE78Q52572588-004A5CF4-EE71-4C3F-9761-7E3E57EF3694Q53435617-45A612E7-3E85-46B0-90F0-EF2AEC10A013Q56225273-FF92EEDE-D884-475C-9A1D-16BE9A1CCFA3
P50
description
onderzoeker
@nl
researcher, ORCID id # 0000-0002-9420-7998
@en
name
Philippe H Hünenberger
@ast
Philippe H Hünenberger
@en
Philippe H Hünenberger
@es
Philippe H Hünenberger
@nl
type
label
Philippe H Hünenberger
@ast
Philippe H Hünenberger
@en
Philippe H Hünenberger
@es
Philippe H Hünenberger
@nl
prefLabel
Philippe H Hünenberger
@ast
Philippe H Hünenberger
@en
Philippe H Hünenberger
@es
Philippe H Hünenberger
@nl
P106
P1153
7003687372
P2456
P31
P496
0000-0002-9420-7998