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Erik Lindahl
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2020 – today
- 2024
- [j24]Magnus Lundborg
, Christian Wennberg
Simulating the Skin Permeation Process of Ionizable Molecules. J. Chem. Inf. Model. 64(13): 5295-5302 (2024) - [i3]Andrey Alekseenko, Szilárd Páll, Erik Lindahl:
GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability. CoRR abs/2405.01420 (2024) - 2023
- [j23]Christian Wennberg
Understanding Drug Skin Permeation Enhancers Using Molecular Dynamics Simulations. J. Chem. Inf. Model. 63(15): 4900-4911 (2023) - [j22]Christian Blau, Linnea Yvonnesdotter
Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach. PLoS Comput. Biol. 19(7) (2023) - 2021
- [c8]Andrey Alekseenko
Experiences With Adding SYCL Support to GROMACS. IWOCL 2021: 17:1 - 2020
- [i2]Szilárd Páll
Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS. CoRR abs/2006.09167 (2020)
2010 – 2019
- 2019
- [j21]Laura Orellana
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces. Bioinform. 35(18): 3505-3507 (2019) - [j20]Mark James Abraham
Sharing Data from Molecular Simulations. J. Chem. Inf. Model. 59(10): 4093-4099 (2019) - [j19]Arne Elofsson
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15(1) (2019) - [c7]Erwin Laure, Olivia Eriksson, Erik Lindahl, Dan S. Henningson:
The Future of Swedish e-Science: SeRC 2.0. eScience 2019: 413-420 - 2018
- [j18]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): 398-404 (2018) - 2017
- [j17]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: 18-31 (2017) - 2016
- [j16]Samira Yazdi, Matthias Stein
The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. PLoS Comput. Biol. 12(1) (2016) - 2015
- [i1]Szilárd Páll, Mark James Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl:
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. CoRR abs/1506.00716 (2015) - 2014
- [j15]Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J. Comput. Chem. 35(3): 260-269 (2014) - [c6]Szilárd Páll
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. EASC 2014: 3-27 - 2013
- [j14]Sander Pronk, Szilárd Páll
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29(7): 845-854 (2013) - 2012
- [j13]Arjun Ray
Improved model quality assessment using ProQ2. BMC Bioinform. 13: 224 (2012) - [j12]Samuel Murail
Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors. PLoS Comput. Biol. 8(10) (2012) - [c5]J. A. Åström, Adam C. Carter
Preparing Scientific Application Software for Exascale Computing. PARA 2012: 27-42 - 2011
- [c4]Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess
Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC 2011: 60:1-60:10 - [c3]Szilárd Páll, Berk Hess
Poster: 3D tixels: a highly efficient algorithm for gpu/cpu-acceleration of molecular dynamics on heterogeneous parallel architectures. SC Companion 2011: 71-72 - 2010
- [j11]Arjun Ray
Model quality assessment for membrane proteins. Bioinform. 26(24): 3067-3074 (2010) - [j10]Per Larsson, Erik Lindahl
A high-performance parallel-generalized born implementation enabled by tabulated interaction rescaling. J. Comput. Chem. 31(14): 2593-2600 (2010) - [j9]Edward J. Bertaccini, Björn Wallner
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): 2248-2255 (2010) - [j8]Peter M. Kasson
Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Comput. Biol. 6(6) (2010)
2000 – 2009
- 2009
- [j7]Pär Bjelkmar
Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. PLoS Comput. Biol. 5(2) (2009) - 2008
- [j6]Edward J. Bertaccini
Effect of Cobratoxin Binding on the Normal Mode Vibration within Acetylcholine Binding Protein. J. Chem. Inf. Model. 48(4): 855-860 (2008) - [c2]Erik Lindahl, Oscar Gustafsson
Architecture-aware design of a decimation filter based on a dual wordlength multiply-accumulate unit. ACSCC 2008: 1897-1901 - 2007
- [j5]Carsten Kutzner, David van der Spoel
Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. 28(12): 2075-2084 (2007) - [j4]Edward J. Bertaccini
Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods. J. Chem. Inf. Model. 47(4): 1572-1579 (2007) - 2006
- [j3]Cyril Azuara, Erik Lindahl
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res. 34(Web-Server-Issue): 38-42 (2006) - [j2]Erik Lindahl
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res. 34(Web-Server-Issue): 52-56 (2006) - [c1]Carsten Kutzner, David van der Spoel
Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI 2006: 404-405 - 2005
- [j1]David van der Spoel
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26(16): 1701-1718 (2005)
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last updated on 2024-10-07 21:23 CEST by the dblp team
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