Erik Lindahl

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 13

Top Topics

Molecular Dynamics Simulations

Columbia University

Scientific Computing

Trajectory Data

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Publications

Andrey Alekseenko, Szilárd Páll, Erik Lindahl
GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. CoRR (2024)
Magnus Lundborg, Christian Wennberg, Erik Lindahl, Lars Norlén
Simulating the Skin Permeation Process of Ionizable Molecules. J. Chem. Inf. Model. 64 (13) (2024)
Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach. PLoS Comput. Biol. 19 (7) (2023)
Christian Wennberg, Magnus Lundborg, Erik Lindahl, Lars Norlén
Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 63 (15) (2023)
Andrey Alekseenko, Szilárd Páll, Erik Lindahl
Experiences With Adding SYCL Support to GROMACS. IWOCL (2021)
Szilárd Páll, Artem A. Zhmurov, Paul Bauer, Mark James Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl
Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. CoRR (2020)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
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, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikael Trellet, Christopher J. Woods, Artem A. Zhmurov
Sharing Data from Molecular Simulations. J. Chem. Inf. Model. 59 (10) (2019)
Erwin Laure, Olivia Eriksson, Erik Lindahl, Dan S. Henningson
The Future of Swedish e-Science: SeRC 2.0. eScience (2019)
Laura Orellana, Johan Gustavsson, Cathrine Bergh, Ozge Yoluk, Erik Lindahl
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinform. 35 (18) (2019)
Olivia Eriksson, Erwin Laure, Erik Lindahl, Dan S. Henningson, Anders Ynnerman
e-Science in Scandinavia - The Case of the Swedish e-Science Research Center. Inform. Spektrum 41 (6) (2018)
Iman Pouya, Sander Pronk, Magnus Lundborg, Erik Lindahl
Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling. Future Gener. Comput. Syst. 71 (2017)
Samira Yazdi, Matthias Stein, Fredrik Elinder, Magnus Andersson, Erik Lindahl
Voltage-Gated Potassium Channel. PLoS Comput. Biol. 12 (1) (2016)
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. CoRR (2015)
Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J. Comput. Chem. 35 (3) (2014)
Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. EASC (2014)
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
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29 (7) (2013)
Samuel Murail, Rebecca J. Howard, Torben Broemstrup, Edward J. Bertaccini, R. Adron Harris, James R. Trudell, Erik Lindahl
Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. PLoS Comput. Biol. 8 (10) (2012)
J. A. Åström, Adam Carter, James Hetherington, K. Ioakimidis, Erik Lindahl, G. Mozdzynski, Rupert W. Nash, Philipp Schlatter, Artur Signell, Jan Westerholm
Preparing Scientific Application Software for Exascale Computing. PARA (2012)
Arjun Ray, Erik Lindahl, Björn Wallner
Improved model quality assessment using ProQ2. BMC Bioinform. 13 (2012)
Szilárd Páll, Berk Hess, Erik Lindahl
Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. SC Companion (2011)
Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl
Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC (2011)
Per Larsson, Erik Lindahl
A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. J. Comput. Chem. 31 (14) (2010)
Edward J. Bertaccini, Björn Wallner, James R. Trudell, Erik Lindahl
Modeling Anesthetic Binding Sites within the Glycine Alpha One Receptor Based on Prokaryotic Ion Channel Templates: The Problem with TM4. J. Chem. Inf. Model. 50 (12) (2010)
Peter M. Kasson, Erik Lindahl, Vijay S. Pande
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput. Biol. 6 (6) (2010)
Arjun Ray, Erik Lindahl, Björn Wallner
Model quality assessment for membrane proteins. Bioinform. 26 (24) (2010)
Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl
Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. PLoS Comput. Biol. 5 (2) (2009)
Erik Lindahl, Oscar Gustafsson
Architecture-aware design of a decimation filter based on a dual wordlength multiply-accumulate unit. ACSCC (2008)
Edward J. Bertaccini, Erik Lindahl, Titia Sixma, James R. Trudell
Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. J. Chem. Inf. Model. 48 (4) (2008)
Edward J. Bertaccini, James R. Trudell, Erik Lindahl
Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. J. Chem. Inf. Model. 47 (4) (2007)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. 28 (12) (2007)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI (2006)
Erik Lindahl, Cyril Azuara, Patrice Koehl, Marc Delarue
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Cyril Azuara, Erik Lindahl, Patrice Koehl, Henri Orland, Marc Delarue
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26 (16) (2005)