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1

Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry

Prof. Dr. Wilfred F. van Gunsteren, Prof. Dr. Herman J. C. Berendsen

Journal:

Angewandte Chemie International Edition

Year:

1990

Language:

english

File:

PDF, 3.39 MB

english, 1990

2

Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations

Thomas C. Beutler, Alan E. Mark, René C. van Schaik, Paul R. Gerber, Wilfred F. van Gunsteren

Journal:

Chemical Physics Letters

Year:

1994

Language:

english

File:

PDF, 1022 KB

english, 1994

3

Accounting for polarization in molecular simulation

Haibo Yu, Wilfred F. van Gunsteren

Journal:

Computer Physics Communications

Year:

2005

Language:

english

File:

PDF, 390 KB

english, 2005

4

The effect of using a polarizable solvent model upon the folding equilibrium of different β-peptides

Lin, Zhixiong, Schmid, Nathan, van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2011

Language:

english

File:

PDF, 1.34 MB

english, 2011

5

A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems

Luty, Brock A., Davis, Malcolm E., Tironi, Ilario G., Van Gunsteren, Wilfred F.

Journal:

Molecular Simulation

Year:

1994

Language:

english

File:

PDF, 696 KB

english, 1994

6

A Comparison of Seven Fast but Approximate Methods to Compute the Free Energy of Deprotonation for Amino Acids in Aqueous Solution

Bürgi, Roland, Läng, Florian, Van Gunsteren, Wilfred F.

Journal:

Molecular Simulation

Year:

2001

Language:

english

File:

PDF, 1.07 MB

english, 2001

7

Algorithms to apply dihedral-angle constraints in molecular or stochastic dynamics simulations

Pechlaner, Maria, van Gunsteren, Wilfred F.

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 1.21 MB

2020

8

Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations

Berweger, Christian D., van Gunsteren, Wilfred F., M�ller-Plathe, Florian

Journal:

Journal of Computational Chemistry

Year:

1997

Language:

english

File:

PDF, 187 KB

english, 1997

9

Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: A molecular dynamics study

Schiffer, Celia A., van Gunsteren, Wilfred F.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1996

Language:

english

File:

PDF, 753 KB

english, 1996

10

Solvent structure at a hydrophobic protein surface

Helena Kovacs, Alan E. Mark, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 228 KB

english, 1997

11

Viscosity dependence of protein dynamics

Regula Walser, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 534 KB

english, 2001

12

Are NMR-Derived Model Structures for β-Peptides Representative for the Ensemble of Structures Adopted in Solution?

Alice Glättli, Wilfred F. van Gunsteren

Journal:

Angewandte Chemie

Year:

2004

Language:

english

File:

PDF, 188 KB

english, 2004

13

A consistent empirical potential for water–protein interactions

Jan Hermans, Herman J. C. Berendsen, Wilfred F. Van Gunsteren, Johan P. M. Postma

Journal:

Year:

1984

Language:

english

File:

PDF, 275 KB

english, 1984

14

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

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 181 KB

english, 2004

15

On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

Markus Christen, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2008

Language:

english

File:

PDF, 150 KB

english, 2008

16

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

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 320 KB

english, 2009

17

Basic ingredients of free energy calculations: A review

Clara D. Christ, Alan E. Mark, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2010

Language:

english

File:

PDF, 159 KB

english, 2010

18

Algorithms for clustering molecular dynamics configurations

Andrew E. Torda, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

1994

Language:

english

File:

PDF, 805 KB

english, 1994

19

Molecular dynamics simulations of peptides containing an unnatural amino acid: Dimerization, folding, and protein binding

Haibo Yu, Xavier Daura, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 298 KB

english, 2004

20

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

Nathan Schmid, Andreas P. Eichenberger, Alexandra Choutko, Sereina Riniker, Moritz Winger, Alan E. Mark, Wilfred F. van Gunsteren

Journal:

European Biophysics Journal

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

21

On the validity of Stokes' law at the molecular level

Regula Walser, Alan E. Mark, Wilfred F. van Gunsteren

Journal:

Chemical Physics Letters

Year:

1999

Language:

english

File:

PDF, 61 KB

english, 1999

22

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

Journal:

Computer Physics Communications

Year:

2012

Language:

english

File:

PDF, 555 KB

english, 2012

23

Decomposition of the Free Energy of a System in Terms of Specific Interactions: Implications for Theoretical and Experimental Studies

Alan E. Mark, Wilfred F. van Gunsteren

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 542 KB

1994

24

Practical Aspects of Free-Energy Calculations: A Review

Hansen, Niels, van Gunsteren, Wilfred F.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 480 KB

english, 2014

25

Development of a simple, self-consistent polarizable model for liquid water

Yu, Haibo, Hansson, Tomas, van Gunsteren, Wilfred F.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 352 KB

english, 2003

26

Computer simulation of a polymer electrolyte: Lithium iodide in amorphous poly(ethylene oxide)

Müller-Plathe, Florian, van Gunsteren, Wilfred F.

Journal:

The Journal of Chemical Physics

Year:

1995

Language:

english

File:

PDF, 489 KB

english, 1995

27

Solvent-dependent conformation and hydrogen-bonding capacity of cyclosporin A: evidence from partition coefficients and molecular dynamics simulations

El Tayar, Nabil, Mark, Alan E., Vallat, Philippe, Brunne, Roger M., Testa, Bernard, van Gunsteren, Wilfred F.

Journal:

Journal of Medicinal Chemistry

Year:

1993

Language:

english

File:

PDF, 1.92 MB

english, 1993

28

A simple, efficient polarizable molecular model for liquid carbon tetrachloride

Kunz, Anna-Pitschna E., Eichenberger, Andreas P., van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2011

Language:

english

File:

PDF, 210 KB

english, 2011

29

The effect of branched side chains on the relative stability of α - and π -helices: a combination of the enveloping distribution sampling and one-step perturbation methods †

Lin, Zhixiong, van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 261 KB

english, 2013

30

On the use of one-step perturbation to investigate the dependence of different properties of liquid water on a variation of model parameters from a single simulation †

Bachmann, Stephan J., Dolenc, Jozica, van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 814 KB

english, 2013

31

Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

Yu, Haibo, van Gunsteren, Wilfred F.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 630 KB

english, 2004

32

On the compatibility of polarisable and non-polarisable models for liquid water

Bachmann, Stephan Jan, van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

33

A Molecular Dynamics Simulation Study of Liquid Carbon Tetrachloride

Tironi, Ilario G., Fontana, Patrick, van Gunsteren, Wilfred F.

Journal:

Molecular Simulation

Year:

1996

Language:

english

File:

PDF, 460 KB

english, 1996

34

Can the stability of protein mutants be predicted by free energy calculations?

Yun-yu, Shi, Mark, Alan E., Cun-xin, Wang, Fuhua, Huang, Berendsen, Herman J.C., Gunsteren, Wilfred F.van

Journal:

Protein Engineering Design and Selection

Year:

1993

Language:

english

File:

PDF, 700 KB

english, 1993

35

Test of a method for sampling the internal degrees of freedom of a flexible solute molecule based on adiabatic decoupling and temperature or force scaling

Kunz, Anna-Pitschna E., Lin, Zhixiong, van Gunsteren, Wilfred F.

Journal:

Molecular Physics

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

36

Parametrization of aliphatic CHn united atoms of GROMOS96 force field

Daura, Xavier, Mark, Alan E., Van Gunsteren, Wilfred F.

Journal:

Journal of Computational Chemistry

Year:

1998

Language:

english

File:

PDF, 203 KB

english, 1998

37

Estimating relative free energies from a single ensemble: Hydration free energies

Sch�fer, Heiko, Van Gunsteren, Wilfred F., Mark, Alan E.

Journal:

Journal of Computational Chemistry

Year:

1999

Language:

english

File:

PDF, 280 KB

english, 1999

38

Reversible peptide folding: Dependence on molecular force field used

Damm, Wolfgang, van Gunsteren, Wilfred F.

Journal:

Journal of Computational Chemistry

Year:

2000

Language:

english

File:

PDF, 312 KB

english, 2000

39

Protein structure prediction force fields: Parametrization with quasi-newtonian dynamics

Patrick Ulrich, Walter Scott, Wilfred F. van Gunsteren, Andrew E. Torda

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 169 KB

english, 1997

40

Generation of pseudonative protein structures for threading

Fred A. Hamprecht, Walter Scott, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 124 KB

english, 1997

41

Folding–unfolding thermodynamics of a β-heptapeptide from equilibrium simulations

Xavier Daura, Wilfred F. van Gunsteren, Alan E. Mark

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 530 KB

english, 1999

42

Molecular dynamics simulations of human α-lactalbumin: Changes to the structural and dynamical properties of the protein at low pH

Lorna J. Smith, Christopher M. Dobson, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 187 KB

english, 1999

43

Herman Berendsen: Researcher, teacher, scholar, colleague, skipper

Wilfred F. van Gunsteren, Jan Hermans

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 17 KB

english, 1999

44

The effect of motional averaging on the calculation of NMR-derived structural properties

Xavier Daura, Iris Antes, Wilfred F. van Gunsteren, Walter Thiel, Alan E. Mark

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 323 KB

english, 1999

45

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

Celia A. Schiffer, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 381 KB

english, 1999

46

Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data

Urs Stocker, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 259 KB

english, 2000

47

Peptidfaltung: Wenn die Simulation das Experiment erreicht

Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, Alan E. Mark

Journal:

Angewandte Chemie

Year:

1999

Language:

german

File:

PDF, 206 KB

german, 1999

48

Die Photoisomerisierung von cis-Stilben folgt nicht dem Weg minimaler Energie

Christian D. Berweger, Wilfred F. van Gunsteren, Florian Müller-Plathe

Journal:

Angewandte Chemie

Year:

1999

Language:

german

File:

PDF, 119 KB

german, 1999

49

Peptide Folding: When Simulation Meets Experiment

Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, Alan E. Mark

Journal:

Angewandte Chemie International Edition

Year:

1999

Language:

english

File:

PDF, 214 KB

english, 1999

50

The Photoisomerization of cis-Stilbene Does Not Follow the Minimum Energy Path

Christian D. Berweger, Wilfred F. van Gunsteren, Florian Müller-Plathe

Journal:

Angewandte Chemie International Edition

Year:

1999

Language:

english

File:

PDF, 99 KB

english, 1999