David van der Spoel

23 papers Journal 21Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output. J. Chem. Inf. Model. Måns K. Rosenbaum, David van der Spoel
2023	J	`jnl`	An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J. Chem. Inf. Model. Kristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel
2020	J	`jnl`	Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. J. Chem. Inf. Model. Leandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel
2020	J	`jnl`	Toward a Computational Ecotoxicity Assay. J. Chem. Inf. Model. Natasha Kamerlin, Mickaël G. Delcey, Sergio Manzetti, David van der Spoel
2019	J	`jnl`	Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
2018	J	`jnl`	Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. J. Chem. Inf. Model. Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel
2017	J	`jnl`	Systematic exploration of multiple drug binding sites. J. Cheminformatics Mónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi
2016	J	`jnl`	Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J. Chem. Inf. Model. Jin Zhang, Badamkhatan Tuguldur, David van der Spoel
2016	J	`jnl`	Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes. J. Chem. Inf. Model. Haiyang Zhang, Chunhua Yin, Hai Yan, David van der Spoel
2016	J	`jnl`	Exploration of Interfacial Hydration Networks of Target-Ligand Complexes. J. Chem. Inf. Model. Norbert Jeszenoi, Mónika Bálint, István Horváth, David van der Spoel, Csaba Hetényi
2015	J	`jnl`	Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J. Chem. Inf. Model. Jin Zhang, Badamkhatan Tuguldur, David van der Spoel
2015	J	`jnl`	Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J. Comput. Chem. Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.
2015	J	`jnl`	Mobility-based prediction of hydration structures of protein surfaces. Bioinform. Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi
2014	J	`jnl`	An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J. Comput. Chem. Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl
2014	J	`jnl`	MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. Bioinform. Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel
2013	J	`jnl`	GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 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
2012	J	`jnl`	GROMACS molecule & liquid database. Bioinform. David van der Spoel, Paul J. van Maaren, Carl Caleman
2012	J	`jnl`	Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations. PLoS Comput. Biol. Daniel S. D. Larsson, Lars Liljas, David van der Spoel
2007	J	`jnl`	Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	—	`conf`	Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
2006	—	`conf`	Protein Folding Properties from Molecular Dynamics Simulations. PARA David van der Spoel, Alexandra Patriksson, M. Marvin Seibert
2005	J	`jnl`	GROMACS: Fast, flexible, and free. J. Comput. Chem. David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
2003	J	`jnl`	Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. J. Comput. Aided Mol. Des. Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, David van der Spoel