David van der Spoel - researchr alias

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Viewing Publication 1 - 22 from 22

2023

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular SimulationKristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel. jcisd, 63(2):412-431, January 2023. [doi]

2020

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular SimulationLeandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel. jcisd, 60(1):322-331, 2020. [doi]

Toward a Computational Ecotoxicity AssayNatasha Kamerlin, Mickaël G. Delcey, Sergio Manzetti, David van der Spoel. jcisd, 60(8):3792-3803, 2020. [doi]

2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systemsArne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist. ploscb, 15(1), 2019. [doi]

2018

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water ModelsHaiyang Zhang, Chunhua Yin, Yang Jiang 0004, David van der Spoel. jcisd, 58(5):1037-1052, 2018. [doi]

2017

Systematic exploration of multiple drug binding sitesMónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi. jcheminf, 9(1), 2017. [doi]

2016

2015

2014

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation programMohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel. bioinformatics, 30(3):439-441, 2014. [doi]

An efficient and extensible format, library, and API for binary trajectory data from molecular simulationsMagnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl. jcc, 35(3):260-269, 2014. [doi]

2013

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkitSander 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. bioinformatics, 29(7):845-854, 2013. [doi]

2012

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics SimulationsDaniel S. D. Larsson, Lars Liljas, David van der Spoel. ploscb, 8(5), 2012. [doi]

GROMACS molecule & liquid databaseDavid van der Spoel, Paul J. van Maaren, Carl Caleman. bioinformatics, 28(5):752-753, 2012. [doi]

2007

Speeding up parallel GROMACS on high-latency networksCarsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller. jcc, 28(12):2075-2084, 2007. [doi]

2006

Improved GROMACS Scaling on Ethernet Switched ClustersCarsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller. pvm 2006: 404-405 [doi]

Protein Folding Properties from Molecular Dynamics SimulationsDavid van der Spoel, Alexandra Patriksson, M. Marvin Seibert. para 2007: 109-115 [doi]

2005

GROMACS: Fast, flexible, and freeDavid van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen. jcc, 26(16):1701-1718, 2005. [doi]

2003

Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, David van der Spoel. jcamd, 17(9):551-565, 2003.

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