David van der Spoel

According to our database, David van der Spoel authored at least 22 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.

Kristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel

J. Chem. Inf. Model., January, 2023

2020

Toward a Computational Ecotoxicity Assay.

Natasha Kamerlin, Mickaël G. Delcey, Sergio Manzetti, David van der Spoel

J. Chem. Inf. Model., 2020

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., 2020

2019

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

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist

PLoS Comput. Biol., 2019

2018

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

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

J. Chem. Inf. Model., 2018

2017

Systematic exploration of multiple drug binding sites.

Mónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi

J. Cheminformatics, 2017

2016

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes.

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

J. Chem. Inf. Model., 2016

Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

Jin Zhang, Badamkhatan Tuguldur, David van der Spoel

J. Chem. Inf. Model., 2016

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes.

Norbert Jeszenoi, Mónika Bálint, István Horváth, David van der Spoel, Csaba Hetényi

J. Chem. Inf. Model., 2016

2015

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

Jin Zhang, Badamkhatan Tuguldur, David van der Spoel

J. Chem. Inf. Model., 2015

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

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

J. Comput. Chem., 2015

Mobility-based prediction of hydration structures of protein surfaces.

Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi

Bioinform., 2015

2014

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.

Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl

J. Comput. Chem., 2014

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.

Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel

Bioinform., 2014

2013

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl

Bioinform., 2013

2012

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations.

Daniel S. D. Larsson, Lars Liljas, David van der Spoel

PLoS Comput. Biol., 2012

GROMACS molecule & liquid database.

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

Bioinform., 2012

2007

Speeding up parallel GROMACS on high-latency networks.

Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller

J. Comput. Chem., 2007

2006

Improved GROMACS Scaling on Ethernet Switched Clusters.

Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller

Proceedings of the Recent Advances in Parallel Virtual Machine and Message Passing Interface, 2006

Protein Folding Properties from Molecular Dynamics Simulations.

David van der Spoel, Alexandra Patriksson, M. Marvin Seibert

Proceedings of the Applied Parallel Computing. State of the Art in Scientific Computing, 2006

2005

GROMACS: Fast, flexible, and free.

David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen

J. Comput. Chem., 2005

2003

Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.

Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, David van der Spoel

J. Comput. Aided Mol. Des., 2003