Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry. - Wilfred F. van Gunsteren; Herman J. C. Berendsen (J. Comput. Aided Mol. Des., 1987)

Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data. - J. Lautz; Horst Kessler; R. Kaptein; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 1987)

Achieving Super Computer Performance with a DSP Array Processor. - Anton Gunzinger; Urs A. Müller; Walter Scott; Bernhard Bäumle; Peter Kohler; Johann vonder Mühll; Florian Müller-Plathe; Wilfred F. van Gunsteren; Walter Guggenbühl (SC, 1992)

Conformational search by potential energy annealing: Algorithm and application to cyclosporin A. - René C. van Schaik; Wilfred F. van Gunsteren; Herman J. C. Berendsen (J. Comput. Aided Mol. Des., 1992)

An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes. - Paul R. Gerber; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 1993)

Local elevation: A method for improving the searching properties of molecular dynamics simulation. - Thomas Huber; Andrew Ernest Torda; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 1994)

Algorithms for Clustering Molecular Dynamics Confogurations. - Andrew Ernest Torda; Wilfred F. van Gunsteren (J. Comput. Chem., 1994)

Force and Cirial of Torsional-Angle-Dependent Potentials. - Henk Bekker; H. J. C. Berendesen; Wilfred F. van Gunsteren (J. Comput. Chem., 1995)

Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations. - Christian D. Berweger; Wilfred F. van Gunsteren; Florian Müller-Plathe (J. Comput. Chem., 1997)

Parametrization of aliphatic CHn united atoms of GROMOS96 force field. - Xavier Daura; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 1998)

Estimating Relative Free Energies from a Single Simulation of the Initial State. - Alan E. Mark; Heiko Schäfer; Haiyan Liu; Wilfred F. van Gunsteren (Computational Molecular Dynamics, 1999)

Estimating relative free energies from a single ensemble: Hydration free energies. - Heiko Schäfer; Wilfred F. van Gunsteren; Alan E. Mark (J. Comput. Chem., 1999)

Factor Xa: Simulation studies with an eye to inhibitor design. - Xavier Daura; Eric E. J. Haaksma; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 2000)

Reversible peptide folding: Dependence on molecular force field used. - Wolfgang Damm; Wilfred F. van Gunsteren (J. Comput. Chem., 2000)

A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. - Vincent Kräutler; Wilfred F. van Gunsteren; Philippe H. Hünenberger (J. Comput. Chem., 2001)

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. - Lukas D. Schuler; Xavier Daura; Wilfred F. van Gunsteren (J. Comput. Chem., 2001)

An improved OPLS-AA force field for carbohydrates. - David B. Kony; Wolfgang Damm; Serge Stoll; Wilfred F. van Gunsteren (J. Comput. Chem., 2002)

Chemical Library Subset Selection Algorithms: A Unified Derivation Using Spatial Statistics. - Fred A. Hamprecht; Walter Thiel; Wilfred F. van Gunsteren (J. Chem. Inf. Comput. Sci., 2002)

A novel approach for designing simple point charge models for liquid water with three interaction sites. - Alice Glättli; Xavier Daura; Wilfred F. van Gunsteren (J. Comput. Chem., 2003)

Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. - Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2003)

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. - Chris Oostenbrink; Alessandra Villa; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 2004)

Accounting for polarization in molecular simulation. - Haibo Yu 003; Wilfred F. van Gunsteren (Comput. Phys. Commun., 2005)

The GROMOS software for biomolecular simulation: GROMOS05. - Markus Christen; Philippe H. Hünenberger; Dirk Bakowies; Riccardo Baron; Roland Bürgi; Daan P. Geerke; Tim N. Heinz; Mika A. Kastenholz; Vincent Kräutler; Chris Oostenbrink; Christine Peter; Daniel Trzesniak; et al. (J. Comput. Chem., 2005)

An improved nucleic acid parameter set for the GROMOS force field. - Thereza A. Soares; Philippe H. Hünenberger; Mika A. Kastenholz; Vincent Kräutler; Thomas Lenz; Roberto D. Lins; Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2005)

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models. - Haibo Yu 003; Daan P. Geerke; Haiyan Liu; Wilfred F. van Gunsteren (J. Comput. Chem., 2006)

Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations. - Yu Zhou 002; Chris Oostenbrink; Aldo Jongejan; Wilfred F. van Gunsteren; Wilfred R. Hagen; Simon W. De Leeuw; Jaap A. Jongejan (J. Comput. Chem., 2006)

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. - Markus Christen; Wilfred F. van Gunsteren (J. Comput. Chem., 2008)

Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation. - Clara D. Christ; Wilfred F. van Gunsteren (J. Comput. Chem., 2009)

On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. - Daan P. Geerke; Sandra Luber; Koni H. Marti; Wilfred F. van Gunsteren (J. Comput. Chem., 2009)

Basic ingredients of free energy calculations: A review. - Clara D. Christ; Alan E. Mark; Wilfred F. van Gunsteren (J. Comput. Chem., 2010)

Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution. - Zhixiong Lin; Haiyan Liu; Wilfred F. van Gunsteren (J. Comput. Chem., 2010)

A new force field for simulating phosphatidylcholine bilayers. - David Poger; Wilfred F. van Gunsteren; Alan E. Mark (J. Comput. Chem., 2010)

A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software. - Nathan Schmid; Mathias Bötschi; Wilfred F. van Gunsteren (J. Comput. Chem., 2010)

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. - Jozica Dolenc; Sereina Riniker; Roberto Gaspari; Xavier Daura; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 2011)

Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields. - Zhixiong Lin; Wilfred F. van Gunsteren; Haiyan Liu (J. Comput. Chem., 2011)

Calculation of binding free energies of inhibitors to plasmepsin II. - Denise Steiner; Chris Oostenbrink; François Diederich; Martina Zürcher; Wilfred F. van Gunsteren (J. Comput. Chem., 2011)

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. - Nathan Schmid; Clara D. Christ; Markus Christen; Andreas P. Eichenberger; Wilfred F. van Gunsteren (Comput. Phys. Commun., 2012)

Free enthalpies of replacing water molecules in protein binding pockets. - Sereina Riniker; Luzi J. Barandun; François Diederich; Oliver Krämer; Andreas Steffen; Wilfred F. van Gunsteren (J. Comput. Aided Mol. Des., 2012)

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. - Niels Hansen; Jozica Dolenc; Matthias Knecht; Sereina Riniker; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

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. - Bruno A. C. Horta; Zhixiong Lin; Wei Huang; Sereina Riniker; Wilfred F. van Gunsteren; Philippe H. Hünenberger (J. Comput. Chem., 2012)

New functionalities in the GROMOS biomolecular simulation software. - Anna-Pitschna E. Kunz; Jane R. Allison; Daan P. Geerke; Bruno A. C. Horta; Philippe H. Hünenberger; Sereina Riniker; Nathan Schmid; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. - Katharina Meier; Nathan Schmid; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations. - Katharina Meier; Walter Thiel; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. - Denise Steiner; Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2012)

On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment. - Zhixiong Lin; Wilfred F. van Gunsteren (J. Comput. Chem., 2013)

Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation. - Zhixiong Lin; Wilfred F. van Gunsteren (J. Comput. Chem., 2013)

Refinement of the application of the GROMOS 54A7 force field to β-peptides. - Zhixiong Lin; Wilfred F. van Gunsteren (J. Comput. Chem., 2013)

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons. - Oliwia M. Szklarczyk; Stephan J. Bachmann; Wilfred F. van Gunsteren (J. Comput. Chem., 2014)

Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. - Michael M. H. Graf; Zhixiong Lin; Urban Bren; Dietmar Haltrich; Wilfred F. van Gunsteren; Chris Oostenbrink (PLoS Comput. Biol., 2014)

Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane. - Oliwia M. Szklarczyk; Eirini Arvaniti; Wilfred F. van Gunsteren (J. Comput. Chem., 2015)

Conformational Properties of the Chemotherapeutic Drug Analogue Epothilone A: How to Model a Flexible Protein Ligand Using Scarcely Available Experimental Data. - Jozica Dolenc; Wilfred F. van Gunsteren; Andrea E. Prota; Michel O. Steinmetz; John H. Missimer (J. Chem. Inf. Model., 2019)

A method to apply bond-angle constraints in molecular dynamics simulations. - Maria Pechlaner; Andreas P. Dorta; Zhixiong Lin; Victor H. Rusu; Wilfred F. van Gunsteren (J. Comput. Chem., 2021)

On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. - Maria Pechlaner; Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2021)

Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. - Wilfred F. van Gunsteren; Chris Oostenbrink (J. Chem. Inf. Model., 2024)

Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach. - Maria Pechlaner; Wilfred F. van Gunsteren; Lorna J. Smith; Bartosz Stankiewicz; Lukas N. Wirz; Niels Hansen (J. Chem. Inf. Model., 2024)

Correction to "Molecular Structure Refinement Based on Residual Dipolar Couplings: A Comparison of the Molecular Rotational-Sampling Method with the Alignment-Tensor Approach". - Maria Pechlaner; Wilfred F. van Gunsteren; Lorna J. Smith; Bartosz Stankiewicz; Lukas N. Wirz; Niels Hansen (J. Chem. Inf. Model., 2025)