Articles

1994

Hünenberger, P.H., Allemann, S. & Vogel, P.
Total asymmetric synthesis of 3-amino-3-deoxy-L-talose and derivatives.
Carbohydr. Res., 257, 175-187 (1994).

1995

Hünenberger, P.H., Mark, A.E. & van Gunsteren, W.F.
Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study.
[journal cover]
Proteins: Struct., Funct., Genet., 21, 196-213 (1995).

van Gunsteren, W.F., Hünenberger, P.H., Kovacs, H., Mark, A.E. & Schiffer, C.
Investigation of protein unfolding and stability by computer simulation.
Phil. Trans. R. Soc. Lond. B., 348, 49-59 (1995).

Hünenberger, P.H., Mark, A.E. & van Gunsteren, W.F.
Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations.
J. Mol. Biol, 252, 492-503 (1995).

van Gunsteren, W.F., Hünenberger, Mark, A.E., Smith, P.E. & Tironi, I.G.
Computer simulation of protein motion.
Comput. Phys. Commun., 91, 305-319 (1995).

1996

Daura, X., Hünenberger, P.H., Mark, A.E. Querol, E., Avilés, F.X. & van Gunsteren, W.F.
Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment, and importance of adequate treatment of electrostatic and internal interaction.
J. Am. Chem. Soc., 118, 6285-6294 (1996).

van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P.K., Mark, A.E., Scott, W.R.P. & Tironi, I.G.
Biomolecular simulation: The GROMOS96 manual and user guide.
Verlag der Fachvereine, Zürich, -, 1-1024 (1996).

1997

Hünenberger, P.H., Granwehr, J.K., Aebischer, J.-N., Ghoneim, N., Haselbach, E. & van Gunsteren, W.F.
Experimental and theoretical approach to hydrogen-bonded diastereomeric interactions in a model complex.
J. Am. Chem. Soc., 119, 7533-7544 (1997).

Hünenberger, P.H. & van Gunsteren, W.F.
Empirical classical interaction functions for molecular simulations.
In "Computer simulation of biomolecular systems, theoretical and experimental applications", Vol. 3, van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J., Eds., Kluwer/Escom Science Publishers, Dordrecht, The Netherlands, 3, 3-82 (1997).

1998

Hünenberger, P.H. & van Gunsteren, W.F.
Alternative schemes for the inclusion of a reaction-field correction into molecular dynamics simulations: Influence on the simulated energetic, structural and dielectric properties of liquid water.
J. Chem. Phys., 108, 6117-6134 (1998).

1999

Hünenberger, P.H. & van Gunsteren, W.F.
Empirical classical force fields for molecular systems.
In "Lecture Notes in Chemistry", Vol 71, Sax, A.F., Ed., Springer Verlag, Berlin, Germany, 71, 177-214 (1999).

Hünenberger, P.H., Helms, V., Narayana, N., Taylor, S.S. & McCammon, J.A.
Determinants of ligand binding to c-AMP dependent protein kinase.
Biochemistry, 38, 2358-2366 (1999).

de Bakker, P.I.W., Hünenberger, P.H. & McCammon, J.A.
Molecular dynamics simulations of the hyperthermophilic protein Sac7d from Sulfolobus acidocaldaricus: Contribution of salt bridges to thermostability.
J. Mol. Biol., 285, 1811-1830 (1999).

Hünenberger, P.H. & McCammon, J.A.
Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: A continuum electrostatics study.
J. Chem. Phys., 110, 1856-1872 (1999).

Hünenberger, P.H. & McCammon, J.A.
Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study.
Biophys. Chem., 78, 69-88 (1999).

Scott, W.R.P., Hünenberger, P.H., Tironi, I.G., Mark, A.E., Billeter, S.R., Fennen, J., Torda, A.E., Huber, T., Krüger, P. & van Gunsteren, W.F.
The GROMOS biomolecular simulation program package.
J. Phys. Chem. A, 103, 3596-3607 (1999).

Baker, N.A., Hünenberger, P.H. & McCammon, J.A.
Polarization around an ion in a dielectric continuum with truncated electrostatic interactions.
[erratum]
J. Chem. Phys., 110, 10679-10692 (1999).

Hünenberger, P.H.
Lattice-sum methods for computing electrostatic interactions in molecular simulations.
In "Simulation and theory of electrostatic interactions in solution: Computational chemistry, biophysics, and aqueous solutions", Pratt, L.R. & Hummer, G., Eds., American Institute of Physics, New York, U.S.A., -, 17-83 (1999).

2000

Weber, W., Hünenberger, P.H. & McCammon, J.A.
Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation.
J. Phys. Chem. B, 104, 3668-3675 (2000).

Hünenberger, P.H.
Optimal charge-shaping functions for the particle-particle--particle-mesh (P3M) method for computing electrostatic interactions in molecular simulations.
J. Chem. Phys., 113, 10464-10476 (2000).

2001

Kräutler, V., van Gunsteren, W.F. & Hünenberger, P.H.
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations.
J. Comput. Chem., 22, 501-508 (2001).

Heinz, T.N., van Gunsteren, W.F. & Hünenberger, P.H.
Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations.
J. Chem. Phys., 115, 1125-1136 (2001).

Walser, R., Hünenberger, P.H. & van Gunsteren, W.F.
Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal.
Proteins: Struct., Funct., Genet., 43, 509-519 (2001).

Wong, C.F., Hünenberger, P.H., Akamine, P., Narayana, N., Diller, T., McCammon, J.A., Taylor, S. & Xuong, N.-H.
Computational analysis of PKA-balanol interactions.
J. Med. Chem., 44, 1530-1539 (2001).

Börjesson, U. & Hünenberger, P.H.
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to simple amines.
J. Chem. Phys., 114, 9706-9719 (2001).

Hünenberger, P.H., Börjesson, U. & Lins, R.D.
Electrostatic interactions in biomolecular systems.
Chimia, 55, 861-866 (2001).

2002

Hünenberger, P.H.
Calculation of the group-based pressure in molecular simulations: I. A general formulation including Ewald and particle-particle--particle-mesh electrostatics.
J. Chem. Phys, 116, 6680-6697 (2002).

Oliva, B. & Hünenberger, P.H.
Calculation of the group-based pressure in molecular simulations: II. Numerical tests and application to liquid water.
J. Chem. Phys, 116, 6698-6909 (2002).

Peter, C., van Gunsteren, W.F. & Hünenberger, P.H.
Solving the Poisson equation for solute-solvent systems using fast Fourier transforms.
J. Chem. Phys., 116, 7434-4451 (2002).

Walser, R., Hünenberger, P.H. & van Gunsteren, W.F.
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.
Proteins: Struct., Funct., Genet., 48, 327-340 (2002).

2003

Gargallo, R., Hünenberger, P.H., Avilés, F.X. & Oliva, B.M
Molecular dynamics simulation of highly-charged proteins: Comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.
Protein Sci., 12, 2161-2172 (2003).

Bergdorf, M., Peter, C. & Hünenberger, P.H.
Influence of cutoff truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: A continuum electrostatics study.
J. Chem. Phys., 119, 9129-9144 (2003).

Börjesson, U. & Hünenberger, P.H.
Effect of mutations involving charged residues on the stability of staphylococcal nuclease: A continuum electrostatics study.
Protein Eng., 16, 831-840 (2003).

Peter, C., van Gunsteren, W.F. & Hünenberger, P.H.
A fast-Fourier-transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: Algorithm and application to ionic solvation and ion-ion interaction.
J. Chem. Phys., 119, 12205-12223 (2003).

2004

Kastenholz, M.A. & Hünenberger, P.H.
Influence of articial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods.
J. Phys. Chem. B, 108, 774-788 (2004).

Lins, R.D., Pereira, C.S. & Hünenberger, P.H.
Trehalose-protein interaction in aqueous solution.
Proteins: Struct., Funct., Bioinf., 55, 177-186 (2004).

Pereira, C.S., Lins, R.D., Chandrasekhar, I., Freitas, L.C.G. & Hünenberger, P.H.
Interaction of the disaccharide trehalose with a phospholipid bilayer: A molecular-dynamics study.
Biophys. J., 86, 2273-2285 (2004).

Kony, D., Damm, W., Stoll, S. & Hünenberger, P.H.,
Explicit-solvent molecular-dynamics simulations of the β(1-3)- and β(1-6)-linked disaccharides β-laminarabiose and β-gentiobiose in water.
J. Phys. Chem. B, 108, 5815-5826 (2004).

Heinz, T.N. & Hünenberger, P.H.
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions.
J. Comput. Chem., 25, 1474-1486 (2004).

Börjesson, U. & Hünenberger, P.H.
pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH.
J. Phys. Chem. B, 108, 13551-13559 (2004).

2005

Hünenberger, P.H.
Thermostat algorithms for molecular dynamics simulations.
Adv. Polymer Sci., 173, 105-149 (2005).

Soares, T.A., Hünenberger, P.H., Kastenholz, M.A., Kräutler, V., Lenz, T., Lins, R.D., Oostenbrink, C. & van Gunsteren, W.F.
An improved nucleic-acid parameter set for the GROMOS force field.
J. Comput. Chem., 26, 725-737 (2005).

Pervushin, K., Vögeli, B., Heinz, T.N. & Hünenberger, P.H.
Measuring 1H-1H and 1H-13C RDCs in methyl groups: Example of pulse sequences with numerically optimized coherence transfer schemes.
J. Magn. Reson., 172, 36-47 (2005).

Kräutler, V., Ämissegger, A., Hünenberger, P.H., Hilvert, D., Hansson, T. & van Gunsteren, W.F.
Use of molecular dynamics in the design and structure determination of a photoinducible β-hairpin
J. Am. Chem. Soc., 127, 4935-4942 (2005).

de Vries, A.H., Chandrasekhar, I., van Gunsteren, W.F. & Hünenberger, P.H.
Molecular dynamics simulations of phospholipid bilayers: Influence of artificial periodicity, system size, and simulation time.
J. Phys. Chem. B, 109, 11643-11652 (2005).

Chandrasekhar, I., Bakowies, D., Glättli, A., Hünenberger, P.H., Pereira, C.S. & van Gunsteren, W.F.
Molecular dynamics simulation of lipid bilayers with GROMOS96: Application of surface tension
Mol. Simul., 31, 543-548 (2005).

Heinz, T.N. & Hünenberger, P.H.
Combining the lattice-sum and reaction-field approaches for evaluating long-range electrostatic interactions in molecular simulations.
J. Chem. Phys., 123, 034107/1-034107/19 (2005).

Lins, R.D. & Hünenberger, P.H.
A new GROMOS force field for hexopyranose-based carbohydrates.
J. Comput. Chem., 26, 1400-1412 (2005).

Christen, M., Hünenberger, P.H., Bakowies, D., Baron, R., Bürgi, R., Geerke, D.P., Heinz, T.N., Kastenholz, M.A., Kräutler, V., Oostenbrink, C., Peter, C., Trzesniak, D. & van Gunsteren, W.F.
The GROMOS software for biomolecular simulation: GROMOS05
J. Comput. Chem., 26, 1719-1751 (2005).

2006

Kastenholz, M.A. & Hünenberger, P.H.
Computation of methodology-independent ionic solvation free energies from molecular simulations: I. The electrostatic potential in molecular liquids
J. Chem. Phys., 124, 124106/1-124106/27 (2006).

Kastenholz, M.A. & Hünenberger, P.H.
Computation of methodology-independent ionic solvation free energies from molecular simulations: II. The hydration free energy of the sodium cation.
J. Chem. Phys., 124, 224501/1-224501/20 (2006).

Kastenholz, M.A. & Hünenberger, P.H.
Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: A continuum electrostatics study.
J. Chem. Phys., 124, 124108/1-124108/12 (2006).

Kräutler, V. & Hünenberger, P.H.
A multiple-timestep algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the timestep size for the fast evaluation of non-bonded interactions in molecular simulations.
J. Comput. Chem., 27, 1163-1176 (2006).

Baron, R., de Vries, A.H., Hünenberger, P.H. & van Gunsteren, W.F.
Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates.
J. Phys. Chem. B, 110, 8464-8473 (2006).

Pereira, C.S., Kony, D., Baron, R., Müller, M., van Gunsteren, W.F. & Hünenberger, P.H.
Conformational and dynamical properties of disaccharides in water: A molecular dynamics study.
[erratum]
Biophys. J., 90, 4337-4344 (2006).

Pereira, C.S. & Hünenberger, P.H.
Interaction of the sugars trehalose, maltose and glucose with a phospholipid bilayer: A comparative molecular dynamics study.
J. Phys. Chem. B, 110, 15572-15581 (2006).

Baron, R., van Gunsteren, W.F. & Hünenberger, P.H.
Estimating the configurational entropy from molecular dynamics simulations: Anharmonicity and correlation corrections to the quasi-harmonic approximation.
Trends Phys. Chem., 11, 87-122 (2006).

Baron, R., de Vries, A.H., Hünenberger, P.H. & van Gunsteren, W.F.
Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations.
J. Phys. Chem. B, 110, 15602-15614 (2006).

Kastenholz, M.A., Schwartz, T.U. & Hünenberger, P.H.
Investigation of the transition between the B and Z conformations of DNA by targeted molecular dynamics simulations with explicit solvation.
Biophys. J., 91, 2976-2990 (2006).

van Gunsteren, W.F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D.P., Glättli, A., Hünenberger, P.H., Kastenholz, M.A., Oostenbrink, C., Schenk, M., Trzesniak, D., van der Vegt, N.F.A. & Yu, H.B.
Biomolecular modelling: Goals, problems, perspectives.
Angew. Chem. Int. Ed. Engl., 45, 4064-4092 (2006).

2007

Kony, D., Damm, W., Stoll, S., van Gunsteren, W.F. & Hünenberger, P.H.
Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water.
Biophys. J., 93, 442-455 (2007).

Kony, D., Hünenberger, P.H. & van Gunsteren W.F.
Molecular dynamics simulations of the native and partially folded states of ubiquitin: Influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics.
Protein Sci., 16, 1101-1118 (2007).

Leite, E.S., Santana, S.R., Hünenberger, P.H., Freitas, L.C.G. & Longo, R.L.
On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution.
J. Mol. Model., 13, 1017-1025 (2007).

Kräutler, V., Müller, M & Hünenberger, P.H.
Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: A molecular dynamics study with the GROMOS 45A4 force field.
Carbohydr. Res., 342, 2097-2124 (2007).

2008

Kräutler, V. & Hünenberger, P.H.
Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: Lattice-sum versus reaction-field electrostatics.
Mol. Simul., 34, 491-499 (2008).

Perić, L., Pereira, C.S., Pérez, S. & Hünenberger, P.H.
Conformation, dynamics and ion-binding properties of single-chain polyuronates: A molecular dynamics study
Mol. Simul., 34, 421-446 (2008).

Pereira, C.S. & Hünenberger, P.H.
The influence of polyhydroxylated compounds on a hydrated phospholipid bilayer: A molecular dynamics study.
Mol. Simul., 34, 403-420 (2008).

Todorova, T., Hünenberger, P.H. & Hutter, J.
Car-Parrinello molecular dynamics simulations of CaCl₂ aqueous solutions.
J. Chem. Theory Comput., 4, 779-789 (2008).

Pereira, C.S. & Hünenberger, P.H.
Effect of trehalose on a phospholipid membrane under mechanical stress.
Biophys. J., 95, 3525-3534 (2008).

2009

Reif, M.M., Kräutler, V., Kastenholz, M.A., Daura,X. & Hünenberger, P.H.
Molecular dynamics simulations of a reversibly-folding β-heptapeptide in methanol: Influence of the treatment of long-range electrostatic interactions.
J. Phys. Chem. B, 113, 3112-3128 (2009).

Müller, C.L., Sbalzarini, I.F., van Gunsteren, W.F., Zagrovic, B. & Hünenberger, P.H.
In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble.
J. Chem. Phys., 130, 214904/1-214904/25 (2009).

Lopez, C.A., Rzepiela, A., de Vries, A.H., Dijkhuizen, L., Hünenberger, P.H. & Marrink, S.J.
The Martini coarse-grained force field: Extension to carbohydrates.
J. Chem. Theory Comput., 5, 3195-3210 (2009).

Baron, R., Hünenberger, P.H. & McCammon, J.A.
Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: Correction terms and convergence properties.
J. Chem. Theory Comput., 5, 3150-3160 (2009).

2010

Hansen, H.S. & Hünenberger, P.H.
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.
J. Comput. Chem., 31, 1-23 (2010).

Kräutler, V., Hiller, S. & Hünenberger, P.H.
Residual structure in a peptide fragment of the outer membrane protein X under denaturing conditions: A molecular dynamics study.
Eur. Biophys. J., 39, 1421-1432 (2010).

Geerke, D.P., van Gunsteren, W.F. & Hünenberger, P.H.
Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: Preferential affinity/exclusion effects and their relevance for bioprotection.
Mol. Simul., 36, 708-728 (2010).

Perić-Hassler, L. & Hünenberger, P.H.
Interaction of alginate single-chain polyguluronate segments with mono- and divalent metal cations: A comparative molecular dynamics study.
Mol. Simul., 36, 778-795 (2010).

Satoh, H., Hansen, H.S., Manabe, S., van Gunsteren, W.F. & Hünenberger, P.H.
Theoretical investigation of solvent effects on glycosylation reactions: Stereoselectivity controlled by preferential conformations of the intermediate oxacarbenium-counterion complex.
J. Chem. Theory Comput., 6, 1783-1797 (2010).

Perić-Hassler, L., Hansen, H.S., Baron, R. & Hünenberger, P.H.
Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
Carbohydr. Res., 345, 1781-1801 (2010).

Horta, B.A.C., Perić-Hassler, L. & Hünenberger, P.H.
Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: A comparative molecular dynamics study.
J. Mol. Graph. Model., 29, 331-346 (2010).

Horta, B.A.C., de Vries, A.H. & Hünenberger, P.H.
Simulating the transition between gel and liquid-crystal phases of lipid bilayers: Dependence of the transition temperature on the hydration level.
J. Chem. Theory Comput., 6, 2488-2500 (2010).

Hansen, H.S., Daura, X. & Hünenberger, P.H.
Enhanced conformational sampling in molecular dynamics simulations of solvated peptides: Fragment-based local elevation umbrella sampling.
J. Chem. Theory Comput., 6, 2598-2621 (2010).

Hansen, H.S. & Hünenberger, P.H.
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.
J. Chem. Theory Comput., 6, 2622-2646 (2010).

2011

Hansen, H.S. & Hünenberger, P.H.
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.
J. Comput. Chem., 32, 998-1032 (2011).

Reif, M.M. & Hünenberger, P.H.
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 solvated ions.
J. Chem. Phys., 134, 144103/1-144103/30 (2011).

Reif, M.M. & Hünenberger, P.H.
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.
J. Chem. Phys., 134, 144104/1-144104/25 (2011).

Keller, B., Hünenberger, P.H. & van Gunsteren, W.F.
An analysis of the validity of Markov state models for emulating the dynamics of classical molecular systems and ensembles.
J. Chem. Theory Comput., 7, 1032-1044 (2011).

Horta, B.A.C., Fuchs, P.F.J., van Gunsteren, W.F. & Hünenberger, P.H.
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.
J. Chem. Theory Comput., 7, 1016-1031 (2011).

Horta, B.A.C. & Hünenberger, P.H.
Enantiometic segregation in the gel phase of lipid bilayers.
J. Am. Chem. Soc., 133, 8464-8465 (2011).

Choutko, A., van Gunsteren, W.F. & Hünenberger, P.H.
Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: Enthalpic and entropic driving forces.
Chem. Phys. Chem., 12, 3214-3223 (2011).

Riniker, S., Christ, C.D., Hansen, H.S., Hünenberger, P.H., Oostenbrink, C., Steiner, D. & van Gunsteren, W.F.
Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.
J. Phys. Chem. B, 115, 13570-13577 (2011).

2012

Riniker, S., Horta, B.A.C., Thijssen, B., Gupta, S., van Gunsteren, W.F. & Hünenberger, P.H.
Temperature dependence of the dielectric permittivity of acetic acid, propionic acid and their methyl esters: A molecular dynamics simulation study.
Chem. Phys. Chem., 13, 1182-1190 (2012).

Kunz, A.-P.E., Allison, J.R., Geerke, D.P., Horta, B.A.C., Hünenberger, P.H., Riniker, S., Schmid, N. & van Gunsteren, W.F.
New functionalities in the GROMOS biomolecular simulation software.
J. Comput. Chem., 33, 340-353 (2012).

Horta, B.A.C., Lin, Z., Huang, W., Riniker, S., van Gunsteren, W.F. & Hünenberger, P.H.
Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two β-peptides in methanol.
J. Comput. Chem., 33, 1907-1917 (2012).

Reif, M.M., Hünenberger, P.H. & Oostenbrink, C.
New interaction parameters for charged amino acid side chains in the GROMOS force field.
J. Chem. Theory Comput., 8, 3705-3723 (2012).

Dahlgren, B., Reif, M.M., Hünenberger, P.H. & Hansen, N.
Calculation of derivative thermodynamic hydration and aqueous partial molar properties of ions based on atomistic simulations.
J. Chem. Theory Comput., 8, 3542-3564 (2012).

Fuchs P.F.J., Hansen, H.S., Hünenberger, P.H. & Horta, B.A.C.
A GROMOS parameter set for vicinal diether functions: Properties of polyethyleneoxide and polyethyleneglycol.
J. Chem. Theory Comput., 8, 3943-3963 (2012).

Hünenberger, P.H., Mark, A.E. & Berendsen, H.J.C.
Wilfred van Gunsteren: 35 years of biomolecular simulation.
[journal cover]
J. Chem. Theory Comput., 8, 3425-3429 (2012).

2013

Laner, M., Horta, B.A.C. & Hünenberger, P.H.
Phase-transition properties of glycerol-monopalmitate lipid bilayers investigated by molecular dynamics simulation: Influence of the system size and force-field parameters.
Mol. Simul., 39, 563-583 (2013).

Hansen, N., Hünenberger, P.H. & van Gunsteren, W.F.
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.
J. Chem. Theory Comput., 9, 1334-1346 (2013).

Wang, D., Ámundadóttir, M.L., van Gunsteren, W.F & Hünenberger, P.H.
Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: A molecular dynamics study of cellobiose stereoisomers.
Eur. Biophys. J., 42, 521-537 (2013).

Rocklin, G.J., Mobley, D.L., Dill, K.A. & Hünenberger, P.H.
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.
[journal cover]
J. Chem. Phys., 139, 184103/1-184103/32 (2013).

2014

Bieler, N.S., Häuselmann, R. & Hünenberger, P.H.
Local elevation umbrella sampling applied to the calculation of alchemical free-energy changes via λ-dynamics: The λ-LEUS scheme.
J. Chem. Theory. Comput., 10, 3006-3022 (2014).

Laner, M., Horta, B.A.C. & Hünenberger, P.H.
Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations.
Eur. Biophys. J., 43, 517-544 (2014).

Bieler, N.S. & Hünenberger, P.H.
Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth.
J. Chem. Phys., 141, 201101/1-201101/5 (2014).

2015

Laner, M., Horta, B.A.C. & Hünenberger, P.H.
Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation.
J. Mol. Graph. Model., 55, 48-64 (2015).

Laner, M. & Hünenberger, P.H.
Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: In quest of the biphasic effect.
J. Mol. Graph. Model., 55, 85-104 (2015).

Laner, M. & Hünenberger, P.H.
Phase-transition properties of glycerol-dipalmitate lipid bilayers investigated using molecular dynamics simulation.
J. Mol. Graph. Model., 59, 136-147 (2015).

Bieler, N.S. & Hünenberger, P.H.
On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.
J. Chem. Phys., 142, 165102/1-165102/17 (2015).

Bieler, N.S., Tschopp, J.P. & Hünenberger, P.H.
Multistate λ-local-elevation umbrella-sampling (MS-λ-LEUS): Method and application to the complexation of cations by crown ethers.
J. Chem. Theory. Comput., 11, 2575-2588 (2015).

Bieler, N.S. & Hünenberger, P.H.
Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI vs. λ-LEUS.
J. Comput. Chem., 36, 1686-1697 (2015).

Szklarczyk, O.M., Bieler, N.S., Hünenberger, P.H. & van Gunsteren, W.F.
Flexible boundaries for multiresolution solvation: An algorithm for spatial multiscaling in molecular dynamics simulations.
J. Chem. Theory Comput, 11, 5447-5463 (2015).

2016

Plazinski, W., Lonardi, A. & Hünenberger, P.H.
Revision of the GROMOS 56A6_CARBO force field for hexopyranose-based carbohydrates: Improving the description of ring-conformational equilibria in oligo- and polysaccharide chains.
J. Comput. Chem., 37, 354-365 (2016).

Horta, B.A.C., Merz, P.T., Fuchs, P.F.J., Dolenc, J., Riniker, S. & Hünenberger, P.H.
A GROMOS-compatible force field for small organic molecules in the condensed phase: The 2016H66 parameter set.
J. Chem. Theory Comput., 12, 3825-3850 (2016).

Reif, M.M. & Hünenberger, P.H.
Origin of asymmetric solvation effects for ions in water and organic solvents investigated using molecular dynamics simulations: The Swain acity-basity scale revisited.
J. Phys. Chem. B, 120, 8485-8517 (2016).

Dolenc, J., Hünenberger, P.H. & Renn, O.
Metrics in research - For better or worse?
[full special issue]
Infozine Special Issue, S1, 1-1 (2016).

Hünenberger, P.H.
Bibliometry: The wizard of O's.
Infozine Special Issue, S1, 9-10 (2016).

2017

Lonardi, A., Oborský, P. & Hünenberger, P.H.
Solvent-modulated influence of intramolecular hydrogen-bonding on the conformational properties of the hydroxymethyl group in glucose and galactose: A molecular dynamics simulation study.
Helv. Chim. Acta, 100, e1600158/1-e1600158/33 (2017).

Senac, C., Urbach, P.W., Kurtisovski, E., Hünenberger, P.H., Horta, B.A.C., Taulier, N. & Fuchs, P.F.J.
Simulating bilayers of nonionic surfactants with the GROMOS-compatible 2016H66 force field.
Langmuir, 33, 10225-10238 (2017).

2018

Hofer, T.S. & Hünenberger, P.H.
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM free-energy simulations of sodium and potassium hydration.
J. Chem. Phys., 148, 222814/1-222814/28 (2018).

Prasetyo, N., Hünenberger, P.H. & Hofer, T.
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.
[journal cover]
J. Chem. Theory Comput., 14, 6443-6459 (2018).

Hünenberger, P.H. & Renn, O.
Surfing versus drilling for knowledge in science - When should you use your computer? When should you use your brain?
[full special issue]
Infozine Special Issue, S2, 2-3 (2018).

Hünenberger, P.H.
Of millimeter paper and machine learning.
Infozine Special Issue, S2, 6-8 (2018).

2019

Gonçalves, Y.M.H., Senac, C., Fuchs, P.F.J., Hünenberger, P.H. & Horta, B.A.C.
Influence of the treatment of non-bonded interactions on the thermodynamic and transport properties of pure liquids calculated using the 2016H66 force field.
J. Chem. Theory Comput., 15, 1806-1826 (2019).

Hahn, D.F. & Hünenberger, P.H.
Alchemical free-energy calculations by multiple-replica λ-dynamics: The conveyor belt thermodynamic integration scheme.
J. Chem. Theory Comput., 15, 2392-2419 (2019).

Hahn, D.F., Milić, J.V. & Hünenberger, P.H.
Vase-kite equilibrium of resorcin[4]arene cavitands investigated using molecular dynamics simulations with ball-and-stick local elevation umbrella sampling.
Helv. Chim. Acta, 102, e1900060/1-e1900060/30 (2019).

2020

Hahn, D.F., König, G. & Hünenberger, P.H.
Overcoming orthogonal barriers in alchemical free energy calculations: On the relative merits of λ-variations, λ-extrapolations, and biasing.
J. Chem. Theory Comput., 16, 1630-1645 (2020).

Hahn, D.F., Zarotiadis, R.A. & Hünenberger, P.H.
The conveyor belt umbrella sampling (CBUS) scheme: Principle and application to the calculation of the absolute binding binding free energies of alkali cations to crown ethers.
J. Chem. Theory Comput., 16, 2474-2493 (2020).

Kubincová, A., Hünenberger, P.H. & Krishnan, M.
Interfacial solvation can explain attraction between like-charged objects in aqueous solution.
J. Chem. Phys., 152, 104713/1-104713/9 (2020).

Kashefolgheta, S., Oliveira, M.P., Rieder, S.R., Horta, B.A.C., Acree Jr., W.E. & Hünenberger, P.H.
Evaluating classical force fields against experimental cross-solvation free energies.
J. Chem. Theory Comput., 16, 7556-7580 (2020).

Oliveira, M.P., Andrey, M., Rieder, S.R., Kern, L., Hahn, D.F., Riniker, S., Horta, B.A.C. & Hünenberger, P.H.
Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: Application to the saturated haloalkanes.
J. Chem. Theory Comput., 16, 7525-7555 (2020).

Kubincová, A., Riniker, S. & Hünenberger, P.H.
Reaction-field electrostatics in molecular dynamics simulations: Development of a conservative scheme compatible with an atomic cutoff.
Phys. Chem. Chem. Phys., 22, 26419-26437 (2020).

König, G., Glaser, N., Schroeder, B., Kubincová, A., Hünenberger, P.H. & Riniker, S.
An alternative to conventional λ-intermediate states in alchemical free energy calculations: λ-Enveloping distribution sampling.
J. Chem. Inf. Model., 60, 5407-5423 (2020).

2021

van Gunsteren, W.F., Daura, X., Fuchs, P.F.J., Hansen, N., Horta, B.A.C., Hünenberger, P.H., Mark, A.E., Pechlaner, M., Riniker, S. & Oostenbrink, C.
On the effect of the various assumptions and approximations used in molecular simulation on the properties of bio-molecular systems: A perspective of issues.
Chem. Phys. Chem., 22, 264-282 (2021).

Kashefolgheta, S., Wang, S., Acree Jr., W.E. & Hünenberger, P.H.
Evaluation of nine condensed-phase force fields of the GROMOS, CHARMM, OPLS, AMBER, and OpenFF families against experimental cross-solvation free energies.
Phys. Chem. Chem. Phys., 23, 13055-13074 (2021).

Oliveira, M.P. & Hünenberger, P.H.
Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: Application to oxygen and nitrogen compounds.
Phys. Chem. Chem. Phys., 23, 17774-17793 (2021).

Kubincová, A., Riniker, S. & Hünenberger, P.H.
Solvent-scaling as alternative to coarse-graining in adaptive-resolution simulations: The adaptive solvent-scaling (AdSoS) scheme.
J. Chem. Phys., 155, 094107/1-094107/21 (2021).

König, G., Ries, B., Hünenberger, P.H. & Riniker, S.
Efficient alchemical intermediate states in free energy calculations using λ-enveloping distribution sampling.
J. Chem. Theory Comput., 17, 5805-5815 (2021).

2022

Gonçalves, Y.M.H., Kashefolgheta, S., Oliveira, M.P., Hünenberger, P.H. & Horta, B.A.C.
Simultaneous parametrization of torsional and third-neighbor interaction terms in force-field development: The LLS-SC algorithm.
J. Comput. Chem., 43, 644-653 (2022).

Ries, B., Rieder, S., Rhiner, C., Hünenberger, P.H. & Riniker, S.
RestraintMaker: A graph-based approach to select distance restraints in free-energy calculations with dual topology.
J. Comput.-Aided Mol. Des., 36, 175-192 (2022).

Rieder, S.R., Ries, B., Champion, C., Barros, E.P., Hünenberger, P.H. & Riniker, S.
Replica-exchange enveloping distribution sampling: Calculation of relative free energies in GROMOS.
Chimia, 76, 327-330 (2022).

Rieder, S., Ries, B., Schaller, K., Champion, C., Barros, E.P., Hünenberger, P.H. & Riniker, S.
Replica-exchange enveloping distribution sampling using generalized AMBER force-field topologies: Application to relative hydration free-energy calculations for large sets of molecules.
J. Chem. Inf. Model., 62, 3043-3056 (2022).

Walker-Gibbons, R., Kubincová, A., Hünenberger, P.H. & Krishnan, M.
The role of surface chemistry in the orientational behaviour of water at an interface.
J. Phys. Chem. B, 126, 4697-4710 (2022).

Rieder, S., Ries, B., Kubincová, A., Champion, C., Barros, E.P., Hünenberger, P.H. & Riniker, S.
Leveraging the sampling efficiency of RE-EDS in OpenMM using a shifted reaction-field with an atom-based cutoff.
J. Chem. Phys., 157, 104117/1-104117/18 (2022).

Oliveira, M.P. & Hünenberger, P.H.
Force fields optimized against experimental data for large compound families using CombiFF: Validation considering non-target properties and polyfunctional compounds.
J. Mol. Graph. Model., 118, 108312/1-108312/10 (2022).

Oliveira, M.P., Gonçalves, Y.M.H., Kashef Ol Gheta, S., Rieder, S.R., Horta, B.A.C. & Hünenberger, P.H.
Comparison of the united- and all-atom representations of (halo)alkanes based on two condensed-phase force fields optimized against the same experimental data set.
J. Chem. Theory Comput., 18, 6757-6778 (2022).

2023

Rieder, S.R., Oliveira, M.P., Riniker, S. & Hünenberger, P.H.
Development of an open-source software for isomer enumeration.
J. Cheminf., 15, 10/1-10/22 (2023).

Oliveira, M.P. & Hünenberger, P.H.
Influence of the choice of a Lennard-Jones combination rule on the simulated properties of organic liquids at optimal force-field parametrization.
J. Chem. Theory Comput. , 19, 2048-2063 (2023).

Kubincová, A., Riniker, S. & Hünenberger, P.H.
Simulation of aqueous solutes using the adaptive solvent-scaling (AdSoS) scheme.
J. Chem. Phys., 159, 234102/1-234102/18 (2023).

2024

Champion, C., Hünenberger, P.H. & Riniker, S.
Multistate method to efficiently account for tautomerism and protonation in alchemical free-energy calculations.
J. Chem. Theory Comput., 20, 4350-4362 (2024).