van der Spoel D

Family name	van der Spoel
Given name	David
Initials	D
ORCID	ORCID 0000-0002-7659-8526
Affiliations	Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden

20 publications

PubMed DOI Crossref

The need to implement FAIR principles in biomolecular simulations.

Amaro RE, Åqvist J, Bahar I, ..., Zacharias M, Orozco M

Nat. Methods 22 (4) 641-645 [2025-04-00; online 2025-04-03]

Lucie Delemotte SciLifeLab Fellow

PubMed DOI Crossref

Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields.

Kříž K, van der Spoel D

J Phys Chem Lett 15 (39) 9974-9978 [2024-10-03; online 2024-09-24]

Quantitative predictions from molecular simulations using explicit or implicit interactions

van der Spoel D, Zhang J, Zhang H

Wiley Interdiscip Rev Comput Mol Sci 12 (1) - [2022-01-00; online 2021-06-22]

PubMed DOI Crossref

The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view.

Assis Silva FC, da Costa Lourenço T, van der Spoel D, ..., Azevedo Dos Reis R, Costa LT

J Chem Phys 155 (4) 044704 [2021-07-28; online 2021-08-04]

PubMed DOI Crossref

A potential for molecular simulation of compounds with linear moieties.

van der Spoel D, Henschel H, van Maaren PJ, Ghahremanpour MM, Costa LT

J Chem Phys 153 (8) 084503 [2020-08-28; online 2020-09-03]

PubMed DOI Crossref

Toward a Computational Ecotoxicity Assay.

Kamerlin N, Delcey MG, Manzetti S, van der Spoel D

J Chem Inf Model 60 (8) 3792-3803 [2020-08-24; online 2020-07-21]

PubMed DOI Crossref

An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra.

Henschel H, van der Spoel D

J Phys Chem Lett 11 (14) 5471-5475 [2020-07-16; online 2020-06-25]

PubMed DOI Crossref

Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields.

Henschel H, Andersson AT, Jespers W, Mehdi Ghahremanpour M, van der Spoel D

J Chem Theory Comput 16 (5) 3307-3315 [2020-05-12; online 2020-04-23]

Towards a Computational Ecotoxicity Assay

Kamerlin N, Delcey MG, Manzetti S, van der Spoel D

- - (-) - [2020-03-06; online 2020-03-06]

PubMed DOI Crossref

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation.

Oliveira Bortot L, Bashardanesh Z, van der Spoel D

J Chem Inf Model 60 (1) 322-331 [2020-01-27; online 2019-12-19]

Role of Host–Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

Yin C, Cui Z, Jiang Y, van der Spoel D, Zhang H

J. Phys. Chem. C 123 (29) 17745-17756 [2019-07-25; online 2019-07-01]

PubMed DOI Crossref

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.

Elofsson A, Hess B, Lindahl E, ..., van der Spoel D, Wallqvist A

PLoS Comput Biol 15 (1) e1006649 [2019-01-00; online 2019-01-17]

PubMed DOI Crossref

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development.

van der Spoel D, Ghahremanpour MM, Lemkul JA

J Phys Chem A 122 (45) 8982-8988 [2018-11-15; online 2018-11-06]

PubMed DOI Crossref

Statistical efficiency of methods for computing free energy of hydration.

Yildirim A, Wassenaar TA, van der Spoel D

J Chem Phys 149 (14) 144111 [2018-10-14; online 2018-10-15]

PubMed DOI Crossref

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models.

Zhang H, Yin C, Jiang Y, van der Spoel D

J Chem Inf Model 58 (5) 1037-1052 [2018-05-29; online 2018-04-18]

PubMed DOI Crossref

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

Ghahremanpour MM, van Maaren PJ, van der Spoel D

Sci Data 5 (-) 180062 [2018-04-10; online 2018-04-10]

PubMed DOI Crossref

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations.

de Oliveira Dos Santos Soares R, Bortot LO, van der Spoel D, Caliri A

J Phys Condens Matter 29 (50) 504002 [2017-12-20; online 2017-11-11]

PubMed DOI Crossref

Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton.

Zhang H, Jiang Y, Yan H, ..., Tan T, van der Spoel D

J Phys Chem Lett 8 (12) 2705-2712 [2017-06-15; online 2017-06-06]

PubMed DOI Crossref

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

Zhang J, Zhang H, Wu T, Wang Q, van der Spoel D

J Chem Theory Comput 13 (3) 1034-1043 [2017-03-14; online 2017-03-06]

Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

Ghahremanpour MM, van Maaren PJ, Ditz JC, Lindh R, van der Spoel D

J. Chem. Phys. 145 (11) 114305 [2016-09-21; online 2016-09-19]

SciLifeLab Data Centre

Publications 9.5.1