van der Spoel lab

The David van der Spoel lab works on the Alexandria Chemistry Toolkit (ACT) a machine learning software to derive force fields for molecular simulation from big data from quantum chemistry (See figure). The software allows to systematically evaluate how changes in the mathematical description of the energy function affect the reproduction of reference data.

The group have published a number of methodological papers describing new potential functions for noble gases, based on highest level quantum chemistry. One article shows the challenging and accurate prediction of the melting point of noble gas crystals (J. Chem. Theory Comput 20 (2024) 2362–2376). In another paper, they discovered that there are large sigma holes at the edge of the OH bond in water (J. Phys. Chem. Letters 158 (2024) 9974). A very recent paper based on machine learning using the ACT challenges the de-facto procedure to determine partial charges needed for molecular simulation. In the near future we hope to publish a complete physics-based force field for the simulation of proteins in solution.

LacI strikes a balance between stability and inducibility

Yuan, Jinwen; Lüking, Malin; Zikrin, Spartak; Sen, Beer Chakra et al.

Part of Nucleic Acids Research, 2026
- DOI for LacI strikes a balance between stability and inducibility
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plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output

Rosenbaum, Måns; Van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 2955-2959, 2026
- DOI for plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output
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Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models

Hosseini, A. Najla; Kriz, Kristian; Van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 2220-2231, 2026
- DOI for Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models
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Quantitative evaluation of anharmonic bond potentials for molecular simulations

van Maaren, Paul J.; Van der Spoel, David

Part of Digital Discovery, p. 824-830, 2025
- DOI for Quantitative evaluation of anharmonic bond potentials for molecular simulations
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Point + Gaussian charge model for electrostatic interactions derived by machine learning

Van der Spoel, David; Hosseini, A. Najla

Part of Physical Chemistry, Chemical Physics - PCCP, p. 13817-13820, 2025
- DOI for Point + Gaussian charge model for electrostatic interactions derived by machine learning
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The need to implement FAIR principles in biomolecular simulations

Amaro, Rommie E.; Åqvist, Johan; Bahar, Ivet; Battistini, Federica et al.

Part of Nature Methods, p. 641-645, 2025
- DOI for The need to implement FAIR principles in biomolecular simulations
Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space

Van der Spoel, David; Marrades, Julián; Kriz, Kristian; Hosseini, A. Najla et al.

Part of Digital Discovery, p. 1925-1935, 2025
- DOI for Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space
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Bayesian three-point water models

Nordman, Alfred T.; Engblom, Stefan; Van der Spoel, David

Part of npj Computational Materials, 2025
- DOI for Bayesian three-point water models
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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

Kriz, Kristian; van Maaren, Paul J.; Van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 2362-2376, 2024
- DOI for Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases
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Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?

Hosseini, A. Najla; van der Spoel, David

Part of The Journal of Physical Chemistry Letters, p. 1079-1088, 2024
- DOI for Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
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Assessment of Climate Impact of Sustainable Forestry Based on Landscape Structure

Prytz, Kjell; Van der Spoel, David

Part of Forests, 2024
- DOI for Assessment of Climate Impact of Sustainable Forestry Based on Landscape Structure
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Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields

Kriz, Kristian; Van der Spoel, David

Part of The Journal of Physical Chemistry Letters, p. 9974-9978, 2024
- DOI for Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields
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Simulations of Amyloid-Forming Peptides in the Crystal State

Hosseini, A. Najla; Van der Spoel, David

Part of The Protein Journal, p. 192-204, 2023
- DOI for Simulations of Amyloid-Forming Peptides in the Crystal State
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Can molecular dynamics be used to simulate biomolecular recognition?

Lüking, Malin; Van der Spoel, David; Elf, Johan; Tribello, Gareth A. A.

Part of Journal of Chemical Physics, 2023
- DOI for Can molecular dynamics be used to simulate biomolecular recognition?
Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

Schmidt, Lisa; Van der Spoel, David; Walz, Marie-Madeleine

Part of ACS Physical Chemistry Au, p. 84-93, 2023
- DOI for Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations
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Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

Balint, Monika; Zsido, Balazs Zoltan; Van der Spoel, David; Hetenyi, Csaba

Part of International Journal of Molecular Sciences, 2022
- DOI for Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design
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The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

Assis Silva, Flavia Cristina; Lourenco, Tuanan da Costa; Van der Spoel, David; Aparicio, Santiago et al.

Part of Journal of Chemical Physics, 2021
- DOI for The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

Gapsys, Vytautas; Yildirim, Ahmet; Aldeghi, Matteo; Khalak, Yuriy et al.

Part of Communications Chemistry, 2021
- DOI for Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches
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Microscopic origins of conductivity in molten salts unraveled by computer simulations

Walz, Marie-Madeleine; Van der Spoel, David

Part of Communications Chemistry, 2021
- DOI for Microscopic origins of conductivity in molten salts unraveled by computer simulations
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Classical molecular dynamics

Brooks, Charles L., III; Case, David A.; Plimpton, Steve; Roux, Benoit et al.

Part of Journal of Chemical Physics, 2021
- DOI for Classical molecular dynamics
Editorial overview: Theory and simulation and their new friends

Shehu, Amarda; Van der Spoel, David

Part of Current opinion in structural biology, 2021
- DOI for Editorial overview: Theory and simulation and their new friends
NMR Refinement and Peptide Folding Using the GROMACS Software

Sinelnikova, Anna; Van der Spoel, David

Part of Journal of Biomolecular NMR, p. 143-149, 2021
- DOI for NMR Refinement and Peptide Folding Using the GROMACS Software
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A potential for molecular simulation of compounds with linear moieties

Van der Spoel, David; Henschel, Henning; van Maaren, Paul J.; Ghahremanpour, Mohammad M. et al.

Part of Journal of Chemical Physics, 2020
- DOI for A potential for molecular simulation of compounds with linear moieties
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Toward a Computational Ecotoxicity Assay

Kamerlin, Natasha; Delcey, Mickaël G; Manzetti, Sergio; Van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 3792-3803, 2020
- DOI for Toward a Computational Ecotoxicity Assay
Propagation of uncertainty in physicochemical data to force field predictions

Yildirim, Ahmet; Ghahremanpour, Mohammad Mehdi; Van der Spoel, David

Part of Physical Review Research, 2020
- DOI for Propagation of uncertainty in physicochemical data to force field predictions
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An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Henschel, Henning; Van der Spoel, David

Part of The Journal of Physical Chemistry Letters, p. 5471-5475, 2020
- DOI for An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra
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Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

Bortot, Leandro Oliveira; Bashardanesh, Zahedeh; Van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 322-331, 2020
- DOI for Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation
Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

Henschel, Henning; Andersson, Alfred T.; Jespers, Willem; Ghahremanpour, Mohammad Mehdi et al.

Part of Journal of Chemical Theory and Computation, p. 3307-3315, 2020
- DOI for Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields
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Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

Yin, Chunhua; Cui, Ziheng; Jiang, Yang; Van der Spoel, David et al.

Part of The Journal of Physical Chemistry C, p. 17745-17756, 2019
- DOI for Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study
Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics

Walz, Marie-Madeleine; Van der Spoel, David

Part of Physical Chemistry, Chemical Physics - PCCP, p. 18516-18524, 2019
- DOI for Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics
Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts

Walz, Marie-Madeleine; Van der Spoel, David

Part of The Journal of Physical Chemistry C, p. 25596-25602, 2019
- DOI for Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts
Systematically improved melting point prediction: a detailed physical simulation model is required

Walz, Marie-Madeleine; Van der Spoel, David

Part of Chemical Communications, p. 12044-12047, 2019
- DOI for Systematically improved melting point prediction: a detailed physical simulation model is required
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Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

Van der Spoel, David; Manzetti, Sergio; Haiyang, Zhang; Klamt, Andreas

Part of ACS Omega, p. 13772-13781, 2019
- DOI for Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods
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Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Elofsson, Arne; Hess, Berk; Lindahl, Erik; Onufriev, Alexey et al.

Part of PloS Computational Biology, 2019
- DOI for Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
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Rotational and Translational Diffusion of Proteins as a Function of Concentration

Bashardanesh, Zahedeh; Elf, Johan; Zhang, Haiyang; Van der Spoel, David

Part of ACS Omega, p. 20654-20664, 2019
- DOI for Rotational and Translational Diffusion of Proteins as a Function of Concentration
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Transient isomers in the photodissociation of bromoiodomethane

Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas et al.

Part of Journal of Chemical Physics, 2018
- DOI for Transient isomers in the photodissociation of bromoiodomethane
Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

Zhang, Haiyang; Yin, Chunhua; Jiang, Yang; van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 1037-1052, 2018
- DOI for Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models
Statistical efficiency of methods for computing free energy of hydration

Yildirim, Ahmet; Wassenaar, Tsjerk A.; Van der Spoel, David

Part of Journal of Chemical Physics, 2018
- DOI for Statistical efficiency of methods for computing free energy of hydration
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Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Van der Spoel, David; Ghahremanpour, Mohammad M.; Lemkul, Justin A.

Part of Journal of Physical Chemistry A, p. 8982-8988, 2018
- DOI for Small Molecule Thermochemistry: A Tool for Empirical Force Field Development
The Alexandria library, a quantum-chemical database of molecular properties for force field development

Ghahremanpour, Mohammad M.; van Maaren, Paul J; Van der Spoel, David

Part of Scientific Data, 2018
- DOI for The Alexandria library, a quantum-chemical database of molecular properties for force field development
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Phase-Transferable Force Field for Alkali Halides

Walz, Marie-Madeleine; Ghahremanpour, Mohammad M.; van Maaren, Paul J.; Van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5933-5948, 2018
- DOI for Phase-Transferable Force Field for Alkali Halides
Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

Ghahremanpour, Mohammad Mehdi; van Maaren, Paul J.; Caleman, Carl; Hutchison, Geoffrey R. et al.

Part of Journal of Chemical Theory and Computation, p. 5553-5566, 2018
- DOI for Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields
Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

Bashardanesh, Zahedeh; van der Spoel, David

Part of Journal of Physical Chemistry B, p. 8018-8027, 2018
- DOI for Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids
Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations

Fischer, Nina M.; Poleto, Marcelo D.; Steuer, Jakob; van der Spoel, David

Part of Nucleic Acids Research, p. 4872-4882, 2018
- DOI for Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
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Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents

Zhang, Jin; Zhang, Haiyang; Wu, Tao; Wang, Qi et al.

Part of Journal of Chemical Theory and Computation, p. 1034-1043, 2017
- DOI for Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents
Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

Lehmann, Laura C.; Hewitt, Graeme; Aibara, Shintaro; Leitner, Alexander et al.

Part of Molecular Cell, p. 847-8590000000, 2017
- DOI for Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1
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Systematic exploration of multiple drug binding sites

Bálint, Mónika; Jeszenői, Norbert; Horváth, István; van der Spoel, David et al.

Part of Journal of Cheminformatics, 2017
- DOI for Systematic exploration of multiple drug binding sites
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Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton

Zhang, Haiyang; Jiang, Yang; Yan, Hai; Yin, Chunhua et al.

Part of The Journal of Physical Chemistry Letters, p. 2705-2712, 2017
- DOI for Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton
Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

dos Santos Soares, Ricardo de Oliveira; Bortot, Leandro Oliveira; van Der Spoel, David; Caliri, Antonio

Part of Journal of Physics, 2017
- DOI for Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations
Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; Ditz, Jonas C.; Lindh, Roland et al.

Part of Journal of Chemical Physics, 2016
- DOI for Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
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Exploration of Interfacial Hydration Networks of Target Ligand Complexes

Jeszenoi, Norbert; Balint, Monika; Horvath, Istvan; van der Spoel, David et al.

Part of Journal of Chemical Information and Modeling, p. 148-158, 2016
- DOI for Exploration of Interfacial Hydration Networks of Target Ligand Complexes
Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes

Zhang, Haiyang; Yin, Chunhua; Yan, Hai; van der Spoel, David

Part of Journal of Chemical Information and Modeling, p. 2080-2092, 2016
- DOI for Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes
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Binding of Pollutants to Biomolecules: A Simulation Study

Yildirim, Ahmet; Zhang, Jin; Manzetti, Sergio; van der Spoel, David

Part of Chemical Research in Toxicology, p. 1679-1688, 2016
- DOI for Binding of Pollutants to Biomolecules: A Simulation Study
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Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

Ghahremanpour, Mohammad Mehdi; van Maaren, Paul J.; Ditz, Jonas C.; Lindh, Roland et al.

Part of Journal of Chemical Physics, 2016
- DOI for Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

Part of Journal of Physical Chemistry B, p. 477-484, 2016
- DOI for Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks
Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization

Zhang, Haiyang; Tan, Tianwei; Van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5103-5113, 2015
- DOI for Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization
Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions

Fischer, Nina M.; van Maaren, Paul J.; Ditz, Jonas C.; Yildirim, Ahmet et al.

Part of Journal of Chemical Theory and Computation, p. 2938-2944, 2015
- DOI for Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions
Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model

Lemkul, Justin A.; Roux, Benoit; van der Spoel, David; MacKerell, Alexander D., Jr.

Part of Journal of Computational Chemistry, p. 1473-1479, 2015
- DOI for Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model
Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

Behzadi, Hadi; Roonasi, Payman; Taghipour, Khatoon Assle; van der Spoel, David et al.

Part of Journal of Molecular Structure, p. 196-202, 2015
- DOI for Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study
Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

Bjorling, Alexander; Niebling, Stephan; Marcellini, Moreno; van der Spoel, David et al.

Part of Journal of Chemical Theory and Computation, p. 780-787, 2015
- DOI for Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations
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Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

Zhang, Jin; Tuguldur, Badamkhatan; van der Spoel, David

Part of JOURNAL OF CHEMICAL INFORMATION AND MODELING, p. 1192-1201, 2015
- DOI for Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation
Mobility-based prediction of hydration structures of protein surfaces

Jeszenoi, Norbert; Horvath, Istvan; Balint, Monika; van der Spoel, David et al.

Part of Bioinformatics, p. 1959-1965, 2015
- DOI for Mobility-based prediction of hydration structures of protein surfaces
Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M. et al.

Part of PLOS ONE, 2015
- DOI for Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
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Thermodynamics of hydronium and hydroxide surface solvation

Hub, Jochen S.; Wolf, Maarten G.; Caleman, Carl; van Maaren, Paul J. et al.

Part of Chemical Science, p. 1745-1749, 2014
- DOI for Thermodynamics of hydronium and hydroxide surface solvation
Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems

Saethre, Bjorn Steen; Hoffmann, Alex C.; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 5606-5615, 2014
- DOI for Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems
Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations

Zhang, Haiyang; Tan, Tianwei; Hetenyi, Csaba; Lv, Yongqin et al.

Part of The Journal of Physical Chemistry C, p. 7163-7173, 2014
- DOI for Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations
CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir

van Lun, Michiel; Hub, Jochen S.; van der Spoel, David; Andersson, Inger

Part of Journal of the American Chemical Society, p. 3165-3171, 2014
- DOI for CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir
Thiamin Function, Metabolism, Uptake, and Transport

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

Part of Biochemistry, p. 821-835, 2014
- DOI for Thiamin Function, Metabolism, Uptake, and Transport
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

Ghahremanpour, Mohammad Mehdi; Arab, Seyed Shahriar; Aghazadeh, Saman Biook; Zhang, Jin et al.

Part of Bioinformatics, p. 439-441, 2014
- DOI for MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program
An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations

Lundborg, Magnus; Apostolov, Rossen; Spångberg, Daniel; Gardenäs, Anders et al.

Part of Journal of Computational Chemistry, p. 260-269, 2014
- DOI for An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations
Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

Zocher, Florian; van der Spoel, David; Pohl, Peter; Hub, Jochen S.

Part of Biophysical Journal, p. 2760-2770, 2013
- DOI for Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes
Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

Marklund, Erik G.; Mahmutovic, Anel; Berg, Otto G.; Hammar, Petter et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19796-19801, 2013
- DOI for Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models
Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View

Lourenco, Tuanan C.; Coelho, Mariny F. C.; Ramalho, Teodorico C.; van der Spoel, David et al.

Part of Environmental Science and Technology, p. 7421-7429, 2013
- DOI for Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
Anopheles gambiae, Anoga-HrTH hormone, free and bound structure: A nuclear magnetic resonance experiment

Mugumbate, Grace; Jackson, Graham E.; van der Spoel, David; Kövér, Katalin E. et al.

Part of Peptides, p. 94-100, 2013
- DOI for Anopheles gambiae, Anoga-HrTH hormone, free and bound structure: A nuclear magnetic resonance experiment
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Pronk, Sander; Pall, Szilard; Schulz, Roland; Larsson, Per et al.

Part of Bioinformatics, p. 845-854, 2013
- DOI for GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Unexpected Effects of Cholesterol on Membrane Permeability

Wennberg, Christian L.; Zocher, Florian; Van der Spoel, David; Pohl, Peter et al.

Part of Biophysical Journal, 2013
- DOI for Unexpected Effects of Cholesterol on Membrane Permeability
beta-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus

Munyuki, Gadzikano; Jackson, Graham E.; Venter, Gerhard A.; Koever, Katalin E. et al.

Part of Biochemistry, p. 7798-7806, 2013
- DOI for beta-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus
Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

Zhang, Haiyang; Tan, Tianwei; Hetenyi, Csaba; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 4542-4551, 2013
- DOI for Quantification of Solvent Contribution to the Stability of Noncovalent Complexes
Organic molecules on the surface of water droplets: an energetic perspective

Hub, Jochen; Caleman, Carl; van der Spoel, David

Part of Physical Chemistry, Chemical Physics - PCCP, p. 9537-9545, 2012
- DOI for Organic molecules on the surface of water droplets: an energetic perspective
GROMACS molecule & liquid database

van der Spoel, David; van Maaren, Paul J.; Caleman, Carl

Part of Bioinformatics, p. 752-753, 2012
- DOI for GROMACS molecule & liquid database
Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation

Yang, Hongqian; Good, David M.; van der Spoel, David; Zubarev, Roman A.

Part of Journal of the American Society for Mass Spectrometry, p. 1319-1325, 2012
- DOI for Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation
Molecular recognition in different environments: β-Cyclodextrin dimer formation in organic solvents

Zhang, H.; Tan, T.; Feng, W.; Van Der Spoel, David

Part of Journal of Physical Chemistry B, p. 12684-12693, 2012
- DOI for Molecular recognition in different environments: β-Cyclodextrin dimer formation in organic solvents
Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil

Saethre, Bjorn Steen; van der Spoel, David; Hoffmann, Alex C.

Part of Journal of Physical Chemistry B, p. 5933-5940, 2012
- DOI for Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil
Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

Wennberg, Christian L.; van der Spoel, David; Hub, Jochen S.

Part of Journal of the American Chemical Society, p. 5351-5361, 2012
- DOI for Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

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

Part of Journal of Chemical Theory and Computation, p. 61-74, 2012
- DOI for Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant
Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules

Zhang, Haiyang; Ge, Chunling; van der Spoel, David; Feng, Wei et al.

Part of Journal of Physical Chemistry B, p. 3880-3889, 2012
- DOI for Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

Larsson, Daniel; Liljas, Lars; van der Spoel, David

Part of PloS Computational Biology, 2012
- DOI for Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
- Download full text (pdf) of Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids

Larsson, Daniel; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 2474-2483, 2012
- DOI for Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids
Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information

Wang, F; Weckert, E; Ziaja, B; Larsson, Daniel S.D. et al.

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2011
- DOI for Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information
Probing (13)C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity

Behzadi, Hadi; Olyai, Mohamad Reza Talei Bavil; van der Spoel, David

Part of Journal of Molecular Modeling, p. 3289-3297, 2011
- DOI for Probing (13)C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity
Trajectory NG: portable, compressed, general molecular dynamics trajectories

Spångberg, Daniel; Larsson, Daniel; van der Spoel, David

Part of Journal of Molecular Modeling, p. 2669-2685, 2011
- DOI for Trajectory NG: portable, compressed, general molecular dynamics trajectories
Proteins, Lipids, and Water in the Gas Phase

van der Spoel, David; Marklund, Erik G.; Larsson, Daniel S. D.; Caleman, Carl

Part of Macromolecular Bioscience, p. 50-59, 2011
- DOI for Proteins, Lipids, and Water in the Gas Phase
Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

Malmerberg, Erik; Omran, Ziad; Hub, Jochen S.; Li, Xuewen et al.

Part of Biophysical Journal, p. 1345-1353, 2011
- DOI for Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin
Subunit Interface Dynamics in Hexadecameric Rubisco

van Lun, Michiel; van der Spoel, David; Andersson, Inger

Part of Journal of Molecular Biology, p. 1083-1098, 2011
- DOI for Subunit Interface Dynamics in Hexadecameric Rubisco
On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

Caleman, Carl; Huldt, Gösta; Maia, Filipe R. N. C.; Ortiz, Carlos et al.

Part of ACS Nano, p. 139-146, 2011
- DOI for On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses
Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding

Mugumbate, Grace; Jackson, Graham E.; van der Spoel, David

Part of Peptides, p. 553-559, 2011
- DOI for Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding
Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Hetenyi, Csaba; van der Spoel, David

Part of Protein Science, p. 880-893, 2011
- DOI for Toward prediction of functional protein pockets using blind docking and pocket search algorithms
Atomistic simulation of ion solvation in water explains surface preference of halides

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

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 6838-6842, 2011
- DOI for Atomistic simulation of ion solvation in water explains surface preference of halides
GROMACS: the road ahead

van der Spoel, David; Hess, Berk

Part of WIREs Computational Molecular Science, p. 710-715, 2011
- DOI for GROMACS: the road ahead
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

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

Part of Biophysical Journal, p. 647-655, 2010
- DOI for Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

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