Publications by authors named "David van der Spoel"

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Correction to "Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases".
Kristian Kříž, Paul J van Maaren, David van der Spoel

J Chem Theory Comput· December 2025

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Point + Gaussian charge model for electrostatic interactions derived by machine learning.
David van der Spoel, A Najla Hosseini

Phys Chem Chem Phys· July 2025

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The need to implement FAIR principles in biomolecular simulations.
Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, David van der Spoel

Nat Methods· April 2025

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Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields.
Kristian Kříž, David van der Spoel

J Phys Chem Lett· October 2024

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Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases.
Kristian Kříž, Paul J van Maaren, David van der Spoel

J Chem Theory Comput· March 2024

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Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
A Najla Hosseini, David van der Spoel

J Phys Chem Lett· February 2024

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Simulations of Amyloid-Forming Peptides in the Crystal State.
A Najla Hosseini, David van der Spoel

Protein J· June 2023

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Can molecular dynamics be used to simulate biomolecular recognition?
Malin Lüking, David van der Spoel, Johan Elf, Gareth A Tribello

J Chem Phys· May 2023

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An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.
Kristian Kříž, Lisa Schmidt, Alfred T Andersson, Marie-Madeleine Walz, David van der Spoel

J Chem Inf Model· January 2023

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Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design.
Mónika Bálint, Balázs Zoltán Zsidó, David van der Spoel, Csaba Hetényi

Int J Mol Sci· June 2022

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The structure of CO and CH at the interface of a poly(urethane urea) oligomer model from the microscopic point of view.
Flavia Cristina Assis Silva, Tuanan da Costa Lourenço, David van der Spoel, Santiago Aparicio, Rodrigo Azevedo Dos Reis

J Chem Phys· July 2021

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NMR refinement and peptide folding using the GROMACS software.
Anna Sinelnikova, David van der Spoel

J Biomol NMR· May 2021

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Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.
Vytautas Gapsys, Ahmet Yildirim, Matteo Aldeghi, Yuriy Khalak, David van der Spoel

Commun Chem· May 2021

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Systematic design of biomolecular force fields.
David van der Spoel

Curr Opin Struct Biol· April 2021

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Editorial overview: Theory and simulation and their new friends.
Amarda Shehu, David Van der Spoel

Curr Opin Struct Biol· April 2021

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Classical molecular dynamics.
Charles L Brooks, David A Case, Steve Plimpton, Benoît Roux, David van der Spoel

J Chem Phys· March 2021

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Microscopic origins of conductivity in molten salts unraveled by computer simulations.
Marie-Madeleine Walz, David van der Spoel

Commun Chem· January 2021

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Toward a Computational Ecotoxicity Assay.
Natasha Kamerlin, Mickaël G Delcey, Sergio Manzetti, David van der Spoel

J Chem Inf Model· August 2020

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A potential for molecular simulation of compounds with linear moieties.
David van der Spoel, Henning Henschel, Paul J van Maaren, Mohammad M Ghahremanpour, Luciano T Costa

J Chem Phys· August 2020

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An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra.
Henning Henschel, David van der Spoel

J Phys Chem Lett· July 2020

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Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields.
Henning Henschel, Alfred T Andersson, Willem Jespers, Mohammad Mehdi Ghahremanpour, David van der Spoel

J Chem Theory Comput· May 2020

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Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation.
Leandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel

J Chem Inf Model· January 2020

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Rotational and Translational Diffusion of Proteins as a Function of Concentration.
Zahedeh Bashardanesh, Johan Elf, Haiyang Zhang, David van der Spoel

ACS Omega· December 2019

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Systematically improved melting point prediction: a detailed physical simulation model is required.
Marie-Madeleine Walz, David van der Spoel

Chem Commun (Camb)· October 2019

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Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods.
David van der Spoel, Sergio Manzetti, Haiyang Zhang, Andreas Klamt

ACS Omega· August 2019

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