research

interests:

• novel algorithms in molecular dynamics simulations
• liquid phase simulation of biooligos

publications:

• Kräutler, V., Heddi, B., Hartmann, B. & Hünenberger, P.H.
  Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: Comparison with experimental data.
  Manuscript in preparation (2008)
  
  
• Explicit-solvent molecular dynamics simulations of a reversibly-folding β-heptapeptide in methanol: Influence of the treatment of long-range electrostatic interactions.
  Kräutler, V., Reif, M., M.A. Kastenholz, Daura, X. & Hünenberger, P.H.
  Manuscript in preparation (2008)
  
  
• Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics
  Vincent Kräutler and Philippe Hünenberger
  Mol. Sim. in press (2008)
  
  
• Conformation, Stability and Solvation of Selected β-Hexopyranoses in Water: A Molecular Dynamics Study
  Vincent Kräutler, Martin Müller and Philippe Hünenberger
  Carbohydr. Res., Volume 342, Issue 14, 2007
  
  
• Classical Molecular Dynamics Simulation: Contributions to Methodology Development and Applications to Biomolecular Systems
  Vincent Kräutler, Diss. ETH 16662, 2006
  
  
• 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
  Vincent Kräutler and Philippe Hünenberger
  J. Comput. Chem., 2006, 1163-1176.
  
  
• The GROMOS software for biomolecular simulation: GROMOS05
  M. Christen, P.H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D.P. Geerke, T.N. Heinz, M.A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, W.F. van Gunsteren
  J. Comput. Chem., 2005, 26, 1719-1751.
  
  
• An Improved Nucleic-Acid Parameter Set for the GROMOS Force Field
  Thereza Soares, Philippe Hünenberger, Mika Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto Lins, Chris Oostenbrink and Wilfred van Gunsteren.
  J. Comput. Chem., 2005, 725–737.
  
  
• Use of Molecular Dynamics in the Design and Structure Determination of a Photoinducible β-Hairpin
  Kräutler, V., Aemissegger, A., Hünenberger, P. H., Hilvert, D., Hansson, T. and van Gunsteren, W.F.
  J. Am. Chem. Soc., 2005, 4935 - 4942.
  
  
• A Photoinducible β-Hairpin
  Aemissegger, A., Kräutler, V., van Gunsteren, W.F., and Hilvert, D.
  J. Am. Chem. Soc., 2005, 2929 - 2936.
  
  
• A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
  J. Comp. Chem., 2001, 501-508.
  Vincent Kräutler, Wilfred F. van Gunsteren, Philippe H. Hünenberger