Wilfred F. van Gunsteren

According to our database1, Wilfred F. van Gunsteren authored at least 50 papers between 1987 and 2015.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2015
Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane.
J. Comput. Chem., 2015

2014
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation.
PLoS Computational Biology, 2014

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons.
J. Comput. Chem., 2014

2013
Refinement of the application of the GROMOS 54A7 force field to β-peptides.
J. Comput. Chem., 2013

Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation.
J. Comput. Chem., 2013

On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment.
J. Comput. Chem., 2013

2012
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9.
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.
J. Comput. Chem., 2012

Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages.
J. Comput. Chem., 2012

New functionalities in the GROMOS biomolecular simulation software.
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.
J. Comput. Chem., 2012

Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution.
J. Comput. Chem., 2012

Free enthalpies of replacing water molecules in protein binding pockets.
J. Comput. Aided Mol. Des., 2012

Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation.
Comput. Phys. Commun., 2012

2011
Calculation of binding free energies of inhibitors to plasmepsin II.
J. Comput. Chem., 2011

Conformational state-specific free energy differences by one-step perturbation: Protein secondary structure preferences of the GROMOS 43A1 and 53A6 force fields.
J. Comput. Chem., 2011

Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities.
J. Comput. Aided Mol. Des., 2011

2010
A GPU solvent-solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software.
J. Comput. Chem., 2010

A new force field for simulating phosphatidylcholine bilayers.
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.
J. Comput. Chem., 2010

Basic ingredients of free energy calculations: A review.
J. Comput. Chem., 2010

2009
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase.
J. Comput. Chem., 2009

Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.
J. Comput. Chem., 2009

2008
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.
J. Comput. Chem., 2008

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.
J. Comput. Chem., 2006

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.
J. Comput. Chem., 2006

2005
An improved nucleic acid parameter set for the GROMOS force field.
J. Comput. Chem., 2005

The GROMOS software for biomolecular simulation: GROMOS05.
J. Comput. Chem., 2005

Accounting for polarization in molecular simulation.
Comput. Phys. Commun., 2005

2004
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.
J. Comput. Chem., 2004

2003
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character.
J. Comput. Chem., 2003

A novel approach for designing simple point charge models for liquid water with three interaction sites.
J. Comput. Chem., 2003

2002
Chemical Library Subset Selection Algorithms: A Unified Derivation Using Spatial Statistics.
J. Chem. Inf. Comput. Sci., 2002

An improved OPLS-AA force field for carbohydrates.
J. Comput. Chem., 2002

2001
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase.
J. Comput. Chem., 2001

A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations.
J. Comput. Chem., 2001

2000
Reversible peptide folding: Dependence on molecular force field used.
J. Comput. Chem., 2000

Factor Xa: Simulation studies with an eye to inhibitor design.
J. Comput. Aided Mol. Des., 2000

1999
Estimating relative free energies from a single ensemble: Hydration free energies.
J. Comput. Chem., 1999

Estimating Relative Free Energies from a Single Simulation of the Initial State.
Proceedings of the Computational Molecular Dynamics: Challenges, Methods, Ideas, 1999

1998
Parametrization of aliphatic CHn united atoms of GROMOS96 force field.
J. Comput. Chem., 1998

1997
Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations.
J. Comput. Chem., 1997

1995
Force and Cirial of Torsional-Angle-Dependent Potentials.
J. Comput. Chem., 1995

1994
Algorithms for Clustering Molecular Dynamics Confogurations.
J. Comput. Chem., 1994

Local elevation: A method for improving the searching properties of molecular dynamics simulation.
J. Comput. Aided Mol. Des., 1994

1993
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes.
J. Comput. Aided Mol. Des., 1993

1992
Conformational search by potential energy annealing: Algorithm and application to cyclosporin A.
J. Comput. Aided Mol. Des., 1992

Achieving Super Computer Performance with a DSP Array Processor.
Proceedings of the Proceedings Supercomputing '92, 1992

1987
Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data.
J. Comput. Aided Mol. Des., 1987

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.
J. Comput. Aided Mol. Des., 1987


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