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)

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 (PVM/MPI, 2006)

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. - Cyril Azuara; Erik Lindahl; Patrice Koehl; Henri Orland; Marc Delarue (Nucleic Acids Res., 2006)

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. - Erik Lindahl; Cyril Azuara; Patrice Koehl; Marc Delarue (Nucleic Acids Res., 2006)

A multi-agent system of evidential reasoning for intelligence analyses. - Erik Lindahl; Stephen O'Hara; Qiuming Zhu (AAMAS, 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)

Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. - Edward J. Bertaccini; James R. Trudell; Erik Lindahl (J. Chem. Inf. Model., 2007)

Architecture-aware design of a decimation filter based on a dual wordlength multiply-accumulate unit. - Erik Lindahl; Oscar Gustafsson (ACSCC, 2008)

Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. - Edward J. Bertaccini; Erik Lindahl; Titia Sixma; James R. Trudell (J. Chem. Inf. Model., 2008)

Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. - Pär Bjelkmar; Perttu S. Niemelä; Ilpo Vattulainen; Erik Lindahl (PLoS Comput. Biol., 2009)

Model quality assessment for membrane proteins. - Arjun Ray; Erik Lindahl; Björn Wallner (Bioinform., 2010)

A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. - Per Larsson; Erik Lindahl (J. Comput. Chem., 2010)

Modeling Anesthetic Binding Sites within the Glycine Alpha One Receptor Based on Prokaryotic Ion Channel Templates: The Problem with TM4. - Edward J. Bertaccini; Björn Wallner; James R. Trudell; Erik Lindahl (J. Chem. Inf. Model., 2010)

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. - Peter M. Kasson; Erik Lindahl; Vijay S. Pande (PLoS Comput. Biol., 2010)

Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. - Szilárd Páll; Berk Hess; Erik Lindahl (SC Companion, 2011)

Copernicus: a new paradigm for parallel adaptive molecular dynamics. - Sander Pronk; Per Larsson; Iman Pouya; Gregory R. Bowman; Imran S. Haque; Kyle Beauchamp; Berk Hess; Vijay S. Pande; Peter M. Kasson; Erik Lindahl (SC, 2011)

Preparing Scientific Application Software for Exascale Computing. - J. A. Åström; Adam C. Carter; James Hetherington; K. Ioakimidis; Erik Lindahl; G. Mozdzynski; Rupert W. Nash; Philipp Schlatter; Artur Signell; Jan Westerholm (PARA, 2012)

Improved model quality assessment using ProQ2. - Arjun Ray; Erik Lindahl; Björn Wallner (BMC Bioinform., 2012)

Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. - Samuel Murail; Rebecca J. Howard; Torben Broemstrup; Edward J. Bertaccini; R. Adron Harris; James R. Trudell; Erik Lindahl (PLoS Comput. Biol., 2012)

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)

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. - Szilárd Páll; Mark James Abraham; Carsten Kutzner; Berk Hess; Erik Lindahl (EASC, 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)

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. - Samira Yazdi; Matthias Stein; Fredrik Elinder; Magnus Andersson; Erik Lindahl (PLoS Comput. Biol., 2016)

Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling. - Iman Pouya; Sander Pronk; Magnus Lundborg; Erik Lindahl (Future Gener. Comput. Syst., 2017)

e-Science in Scandinavia - The Case of the Swedish e-Science Research Center. - Olivia Eriksson; Erwin Laure; Erik Lindahl; Dan S. Henningson; Anders Ynnerman (Inform. Spektrum, 2018)

The Future of Swedish e-Science: SeRC 2.0. - Erwin Laure; Olivia Eriksson; Erik Lindahl; Dan S. Henningson (eScience, 2019)

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. - Laura Orellana; Johan Gustavsson; Cathrine Bergh; Ozge Yoluk; Erik Lindahl (Bioinform., 2019)

Effective degrees of freedom for surface finish defect detection and classification. - Natalya Pya Arnqvist; Blaise Ngendangenzwa; Erik Lindahl; Leif Nilsson; Jun Yu 005 (CoRR, 2019)

Sharing Data from Molecular Simulations. - Mark James Abraham; Rossen Apostolov; Jonathan Barnoud; Paul Bauer; Christian Blau; Alexandre M. J. J. Bonvin; Matthieu Chavent; John D. Chodera; Karmen Condic-Jurkic; Lucie Delemotte; Helmut Grubmüller; Rebecca J. Howard; et al. (J. Chem. Inf. Model., 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)

Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. - Szilárd Páll; Artem A. Zhmurov; Paul Bauer; Mark James Abraham; Magnus Lundborg; Alan Gray; Berk Hess; Erik Lindahl (CoRR, 2020)

Experiences With Adding SYCL Support to GROMACS. - Andrey Alekseenko; Szilárd Páll; Erik Lindahl (IWOCL, 2021)

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Emanuele Vitali; Cristina Silvano; Bruno Guindani; Danilo Ardagna; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; Jan Martinovic; et al. (CF, 2023)

Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach. - Christian Blau; Linnea Yvonnesdotter; Erik Lindahl (PLoS Comput. Biol., 2023)

Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. - Christian Wennberg; Magnus Lundborg; Erik Lindahl; Lars Norlén (J. Chem. Inf. Model., 2023)

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Yuedong Zhang; Emanuele Vitali; Bruno Guindani; Danilo Ardagna; Cristina Silvano; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; et al. (CF (Companion), 2024)

GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. - Andrey Alekseenko; Szilárd Páll; Erik Lindahl (CoRR, 2024)

Simulating the Skin Permeation Process of Ionizable Molecules. - Magnus Lundborg; Christian Wennberg; Erik Lindahl; Lars Norlén (J. Chem. Inf. Model., 2024)

Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins. - Erik Lindahl; Ran Friedman (J. Chem. Inf. Model., 2025)

Lossy Compression of Scientific Data: Applications Constrains and Requirements. - Franck Cappello; Allison H. Baker; Ebru Bozda; Martin Burtscher; Kyle Chard; Sheng Di; Paul Christopher O. Grady; Peng Jiang 004; Shaomeng Li; Erik Lindahl; Peter Lindstrom 001; Magnus Lundborg; et al. (CoRR, 2025)