David van der Spoel

Research interests

Publications

• Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents

  Journal of Chemical Theory and Computation · 2017 · 10.1021/acs.jctc.7b00169

• Water Determines the Structure and Dynamics of Proteins

  Chemical Reviews · 2016 · 10.1021/acs.chemrev.5b00664

• Thiamin Function, Metabolism, Uptake, and Transport

  Biochemistry · 2014 · 10.1021/bi401618y

• Gromacs User Manual Version 4.6

  · 2013

• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

  Bioinformatics · 2013 · https://doi.org/10.1093/bioinformatics/btt055

• Atomistic simulation of ion solvation in water explains surface preference of halides

  Proceedings of the National Academy of Sciences · 2011 · 10.1073/pnas.1017903108

• Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

  Journal of Chemical Theory and Computation · 2011 · 10.1021/ct200731v

• g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

  Journal of Chemical Theory and Computation · 2010 · https://doi.org/10.1021/ct100494z

• A temperature predictor for parallel tempering simulations

  Physical Chemistry Chemical Physics · 2008 · 10.1039/b716554d

• GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

  Journal of Chemical Theory and Computation · 2008 · https://doi.org/10.1021/ct700301q

• Blind docking of drug‐sized compounds to proteins with up to a thousand residues

  FEBS Letters · 2006 · 10.1016/j.febslet.2006.01.074

• Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

  The Journal of Physical Chemistry B · 2006 · 10.1021/jp0572535

• Femtosecond diffractive imaging with a soft-X-ray free-electron laser

  Nature Physics · 2006 · 10.1038/nphys461

• Clocking Femtosecond X Rays

  Physical Review Letters · 2005 · 10.1103/physrevlett.94.114801

• The Origin of Layer Structure Artifacts in Simulations of Liquid Water

  Journal of Chemical Theory and Computation · 2005 · 10.1021/ct0502256

• Atomic-Scale Visualization of Inertial Dynamics

  Science · 2005 · 10.1126/science.1107996

• GROMACS: Fast, flexible, and free

  Journal of Computational Chemistry · 2005 · https://doi.org/10.1002/jcc.20291

• Dynamic properties of water/alcohol mixtures studied by computer simulation

  The Journal of Chemical Physics · 2003 · 10.1063/1.1607918

• Efficient docking of peptides to proteins without prior knowledge of the binding site

  Protein Science · 2002 · 10.1110/ps.0202302

• GROMACS 3.0: a package for molecular simulation and trajectory analysis

  Journal of Molecular Modeling · 2001 · https://doi.org/10.1007/s008940100045

• Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation

  The Journal of Physical Chemistry B · 2000 · 10.1021/jp001268f

• Potential for biomolecular imaging with femtosecond X-ray pulses

  Nature · 2000 · 10.1038/35021099

• A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field

  The Journal of Chemical Physics · 1998 · 10.1063/1.476482

• GROMACS: A message-passing parallel molecular dynamics implementation

  Computer Physics Communications · 1995 · https://doi.org/10.1016/0010-4655(95)00042-e

• GROMACS - A PARALLEL COMPUTER FOR MOLECULAR-DYNAMICS SIMULATIONS

  University of Groningen research database (University of Groningen / Centre for Information Technology) · 1993

Current projects

No projects listed.