van der Spoel lab

"…Everything that living things do can be understood in terms of the jiggling and wiggling of atoms…" is a fame quote by Richard Feynman. Although it is easier said than done my group is working hard to make it possible to predict the " jiggling and wiggling of atoms" using computer simulation based on accurate physical models. With these and other models we study biological systems, e.g. virus particles as well as partial virus capsids in order to understand virus infection and budding at the molecular level. Finally we are studying how pollutants interfere with biological receptors and DNA.

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Research projects

"…Everything that living things do can be understood in terms of the jiggling and wiggling of atoms…" is a fame quote by Richard Feynman. It is easier said than done however. My group is working hard to make this happen. The long-term goals of my research group are therefore

to create physical models (force fields) of compounds and molecules that faithfully reproduce the (free) energies of these compounds,
to implement tools in the GROMACS (http://www.gromacs.org) package for simulations using these models,
to develop and implement tools for the analysis of structural, dynamic and energetic properties of molecular systems and
to perform systematic benchmarks of the predictive power of existing force fields and quantum-chemistry theories with the purpose of generating reference systems for the development of better force fields.

Simultaneously we are using traditional as well as more modern force fields to study a range of systems:

Simulations of entire virus particles as well as partial virus capsids are performed to study virus infection and budding.
Simulations of RNA in solution and in virus particles.
Systematic docking and binding calculations are done to understand how pollutants interfere with biological receptors and DNA.

Welcome to our external homepage

Group members

Group members: David Van der Spoel

Publications

Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?

Hosseini, A. Najla; van der Spoel, David

Part of Journal of Physical Chemistry Letters, p. 1079-1088, 2024
- DOI for Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
- Download full text (pdf) of Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
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
- Download full text (pdf) of Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases
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?
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
- Download full text (pdf) of Simulations of Amyloid-Forming Peptides in the Crystal State
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
- Download full text (pdf) of Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations
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
- Download full text (pdf) of Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design
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
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
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
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
- Download full text (pdf) of Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches
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
- Download full text (pdf) of Microscopic origins of conductivity in molten salts unraveled by computer simulations
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
- Download full text (pdf) of NMR Refinement and Peptide Folding Using the GROMACS Software
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
- Download full text (pdf) of Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields
An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Henschel, Henning; Van der Spoel, David

Part of Journal of Physical Chemistry Letters, p. 5471-5475, 2020
- DOI for An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra
- Download full text (pdf) of An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra
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
- Download full text (pdf) of A potential for molecular simulation of compounds with linear moieties
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
- Download full text (pdf) of Propagation of uncertainty in physicochemical data to force field predictions
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
- Download full text (pdf) of Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
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
- Download full text (pdf) of Systematically improved melting point prediction: a detailed physical simulation model is required
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
- Download full text (pdf) of Rotational and Translational Diffusion of Proteins as a Function of Concentration
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
- Download full text (pdf) of Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods
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
- Download full text (pdf) of Statistical efficiency of methods for computing free energy of hydration
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
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
- Download full text (pdf) of The Alexandria library, a quantum-chemical database of molecular properties for force field development
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
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
- Download full text (pdf) of Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
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 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
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
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
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
- Download full text (pdf) of Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1
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
- Download full text (pdf) of Systematic exploration of multiple drug binding sites
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
- Download full text (pdf) of 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
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
- Download full text (pdf) of Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes
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
- Download full text (pdf) of Binding of Pollutants to Biomolecules: A Simulation Study
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
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
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
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
- Download full text (pdf) of Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations
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
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
- Download full text (pdf) of Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
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
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
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
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
GROMACS: the road ahead

van der Spoel, David; Hess, Berk

Part of Wiley Interdisciplinary Reviews: Computational Molecular Science, p. 710-715, 2011
- DOI for GROMACS: the road ahead
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
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
g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

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

Part of Journal of Chemical Theory and Computation, p. 3713-3720, 2010
- DOI for g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates
Hawk: the image reconstruction package for coherent X-ray diffractive imaging

Maia, Filipe R. N. C.; Ekeberg, Tomas; van der Spoel, David; Hajdu, Janos

Part of Journal of applied crystallography, p. 1535-1539, 2010
- DOI for Hawk: the image reconstruction package for coherent X-ray diffractive imaging
Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo

Friemann, Rosmarie; Larsson, Daniel S. D.; Wang, Yaofeng; van der Spoel, David

Part of Journal of the American Chemical Society, p. 16606-16607, 2009
- DOI for Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo
Structural variability and the incoherent addition of scattered intensities in single-particle diffraction

Maia, Filipe R. N. C.; Ekeberg, Tomas; Timneanu, Nicusor; van der Spoel, David et al.

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, p. 31905, 2009
- DOI for Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study

Wang, Yaofeng; Larsson, Daniel S D; van der Spoel, David

Part of Biochemistry, p. 1006-1015, 2009
- DOI for Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study
A density functional study of N-15 chemical shielding tensors in quinolines

Behzadi, Hadi; Esrafili, D; Beheshtian, Javad; Hadipour, L et al.

Part of Chemical Physics Letters, p. 196-200, 2009
- DOI for A density functional study of N-15 chemical shielding tensors in quinolines
Structural stability of electrosprayed proteins: temperature and hydration effects

Marklund, Erik G.; Larsson, Daniel S. D.; van der Spoel, David; Patriksson, Alexandra et al.

Part of Physical Chemistry, Chemical Physics - PCCP, p. 8069-8078, 2009
- DOI for Structural stability of electrosprayed proteins: temperature and hydration effects
Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP)

Jackson, Graham E; Mabula, Andre N; Stone, Shane R; Gäde, Gerd et al.

Part of Peptides, p. 557-564, 2009
- DOI for Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP)
Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex

Behzadi, Hadi; van der Spoel, David; Esrafili, Mehdi D; Parsafar, Gholam Abbas et al.

Part of Biophysical Chemistry, p. 200-206, 2008
- DOI for Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

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

Part of Journal of Chemical Theory and Computation, p. 435-447, 2008
- DOI for GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

People

David van der Spoel, Ph. D., Professor

Marie-Madeleine Walz, Ph.D., Postdoc

Alfred Andersson, Ph.D. student

Kristian Kriz, Ph.D., Postdoc

Paul J. van Maaren, M.Sc. Visiting scientist

Contact

www.folding.bmc.uu.se