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David van der Spoel

David van der Spoel

D-Index & Metrics

Chemistry

D-Index
65
Citations
75144
World Ranking
7523
National Ranking
99

Overview

David van der Spoel is affiliated with Uppsala University in Sweden and has contributed extensively to the fields of physics and chemistry, focusing on areas including atomic and molecular physics, molecular biology, spectroscopy, materials chemistry, and physical and theoretical chemistry.

Their research interests cover a diverse range of main topics such as:

  • Protein Structure and Dynamics
  • Spectroscopy and Quantum Chemical Studies
  • Computational Drug Discovery Methods
  • Advanced Chemical Physics Studies
  • Enzyme Structure and Function
  • Mass Spectrometry Techniques and Applications
  • Quantum, superfluid, helium dynamics

David van der Spoel has published extensively in scientific journals, frequently appearing in venues such as:

  • The Journal of Chemical Physics
  • The Journal of Physical Chemistry Letters
  • Zenodo (CERN European Organization for Nuclear Research)
  • Communications Chemistry
  • Journal of Chemical Theory and Computation

Some of their recent papers include:

  • "Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches" (2021), published in Communications Chemistry
  • "Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields" (2020), published in Journal of Chemical Theory and Computation
  • "Classical molecular dynamics" (2021), published in The Journal of Chemical Physics
  • "Systematic design of biomolecular force fields" (2020), published in Current Opinion in Structural Biology
  • "Quantitative predictions from molecular simulations using explicit or implicit interactions" (2021), published in Wiley Interdisciplinary Reviews Computational Molecular Science

Their work often brings collaboration with several co-authors, including:

  • Marie-Madeleine Walz
  • Kristian Kříž
  • Paul J. van Maaren
  • A. Hosseini
  • Henning Henschel

Best Publications

  • GROMACS: Fast, flexible, and free

    David Van Der Spoel;Erik Lindahl;Berk Hess;Gerrit Groenhof

  • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

    Berk Hess;Carsten Kutzner;David van der Spoel;Erik Lindahl

  • GROMACS 4.5

    Sander Pronk;Szilárd Páll;Szilárd Páll;Roland Schulz;Roland Schulz;Per Larsson

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

    E. Lindahl;B Hess;D. van der Spoel

  • Potential for biomolecular imaging with femtosecond X-ray pulses

    Richard Neutze;Remco Wouts;David van der Spoel;Edgar Weckert

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

    Jochen S. Hub;Bert L. de Groot;David van der Spoel

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

    Henry N. Chapman;Henry N. Chapman;Anton Barty;Michael J. Bogan;Sébastien Boutet;Sébastien Boutet;Sébastien Boutet

  • Water Determines the Structure and Dynamics of Proteins

    Marie-Claire Bellissent-Funel;Ali Hassanali;Martina Havenith;Richard Henchman

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

    Carl Caleman;Paul J. van Maaren;Minyan Hong;Jochen S. Hub

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

    David van der Spoel;Paul J. van Maaren;Herman J. C. Berendsen

  • A temperature predictor for parallel tempering simulations

    Alexandra Patriksson;David van der Spoel

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

    Csaba Hetényi;David van der Spoel

  • Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

    David van der Spoel;Paul J van Maaren;Per Larsson;Nicusor Timneanu

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

    Csaba Hetényi;David van der Spoel

  • Thiamin Function, Metabolism, Uptake, and Transport

    Sergio Manzetti;Jin Zhang;Jin Zhang;David van der Spoel

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

    Erik J. W. Wensink;Alex C. Hoffmann;Paul J. van Maaren;David van der Spoel

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

    David van der Spoel;Paul J. van Maaren

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

    Jin Zhang;Haiyang Zhang;Tao Wu;Qi Wang

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

    Carl Caleman;Jochen S. Hub;Paul J. van Maaren;David van der Spoel

  • Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

    Oliver F. Lange;David van der Spoel;Bert L. de Groot

  • Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials

    Paul J. van Maaren and;David van der Spoel

Frequent Co-Authors

Erik Lindahl
Erik Lindahl Stockholm University
Tianwei Tan
Tianwei Tan Beijing University of Chemical Technology
Richard Neutze
Richard Neutze University of Gothenburg
Bert L. de Groot
Bert L. de Groot Max Planck Society
Henry N. Chapman
Henry N. Chapman Universität Hamburg
Roman A. Zubarev
Roman A. Zubarev Karolinska Institute
Alex C. Hoffmann
Alex C. Hoffmann University of Bergen
Peter Pohl
Peter Pohl Johannes Kepler University of Linz
Michael Wulff
Michael Wulff European Synchrotron Radiation Facility
Per Jemth
Per Jemth Uppsala University

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