PN 3

SimTech EXC 2075 Project Network 3 "Data-integrated model reduction for particles and continua"

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1 to 10 of 793 Results

Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning Apr 16, 2025 - PN 3-11 Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Korn, Viktoria Helena, 2025, "Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning", https://doi.org/10.18419/DARUS-4134, DaRUS, V1 The simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput.. In details: simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top...
simulations.tar.gz Apr 16, 2025 - Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning Gzip Archive - 3.5 GB - MD5: 29446eb0163201b09183cd448e4fc350 Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top (topology) files. GROMACS 2021 or 2023 was used for the simulations (see paper for details). Additionally, ART-SM and Backward mapping files from coarse-grained to atomistic resolution are included.
workflows.tar.gz Apr 16, 2025 - Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning Gzip Archive - 178.8 KB - MD5: 35b10d2aa63dd1e4aef4aeaa202c34df Snakefiles and python/bash scripts to reproduce the results in the paper. The actual results are not included.
Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Nov 7, 2024 - PN 3-11 Korn, Viktoria Helena; Pluhackova, Kristyna, 2024, "Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'", https://doi.org/10.18419/DARUS-4474, DaRUS, V1 Simulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE). In detail: charmm36-july2017.ff simulation directory for GROMACS 202X used and useful gromacs files (topologies and mdp files) jupyter noteb...
01_charmm36_forcefield.tar.gz Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Gzip Archive - 860.5 KB - MD5: 347ba6c33c95d395b30dc59e99c60c4c
02_analysis.tar.gz Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Gzip Archive - 459.8 MB - MD5: b55ce7d1f3f06816287bc7891c318957
03_gsdmd_monomer_ecoli.tar.gz Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Gzip Archive - 4.7 GB - MD5: 1041add93f9fda86900bca667e4ea81d
04_gsdmd_monomer_popc30chol.tar.gz Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Gzip Archive - 724.1 MB - MD5: 049e51e7eefabd3bcbbfaf8c0755bc5c
05_7mer-arc_ecoli.tar.gz Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3' Gzip Archive - 131.6 MB - MD5: ca0ec7d87ca25cb21bb50f3a6a89a65b
Replication Data for: Origin of the yield stress anomaly in L12 intermetallics unveiled with physically informed machine-learning potentials Oct 8, 2024 - PN 3-10 Xu, Xiang, 2024, "Replication Data for: Origin of the yield stress anomaly in L12 intermetallics unveiled with physically informed machine-learning potentials", https://doi.org/10.18419/DARUS-4480, DaRUS, V1 Data for the manuscript "Origin of the yield stress anomaly in L12 intermetallics unveiled with physically-informed machine-learning potentials", https://doi.org/10.1016/j.actamat.2024.120423. This data set contains: 1) the utilized moment-tensor-potentials (MTP) and the corresponding training sets; 2) The atomistic structure of 2delta Kear-Wilsdor...

Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning

Apr 16, 2025 - PN 3-11

Pluhackova, Kristyna; Pfaendner, Christian; Unger, Benjamin; Korn, Viktoria Helena, 2025, "Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning", https://doi.org/10.18419/DARUS-4134, DaRUS, V1

The simulation files, molecule topologies, and analysis workflows required to generate the results of our paper 'ART-SM: Boosting Fragment-Based Backmapping by Machine Learning' published in J. Chem. Theory Comput.. In details: simulations.tar.gz: Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top...

simulations.tar.gz

Apr 16, 2025 - Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning

Gzip Archive - 3.5 GB -

Contains the pdb (molecular structure), xtc (trajectory), mdp (MD parameters), itp (topology), and top (topology) files. GROMACS 2021 or 2023 was used for the simulations (see paper for details). Additionally, ART-SM and Backward mapping files from coarse-grained to atomistic resolution are included.

workflows.tar.gz

Apr 16, 2025 - Data for: ART-SM: Boosting Fragment-Based Backmapping by Machine Learning

Gzip Archive - 178.8 KB -

Snakefiles and python/bash scripts to reproduce the results in the paper. The actual results are not included.

Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Nov 7, 2024 - PN 3-11

Korn, Viktoria Helena; Pluhackova, Kristyna, 2024, "Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'", https://doi.org/10.18419/DARUS-4474, DaRUS, V1

Simulation files, molecular structures and trajectories, and jupyter notebooks used for analysis underlaying our publication on membrane insertion of monomeric gasdermin D to E. coli polar lipid extract (PLE). In detail: charmm36-july2017.ff simulation directory for GROMACS 202X used and useful gromacs files (topologies and mdp files) jupyter noteb...

01_charmm36_forcefield.tar.gz

Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Gzip Archive - 860.5 KB -

02_analysis.tar.gz

Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Gzip Archive - 459.8 MB -

03_gsdmd_monomer_ecoli.tar.gz

Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Gzip Archive - 4.7 GB -

04_gsdmd_monomer_popc30chol.tar.gz

Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Gzip Archive - 724.1 MB -

05_7mer-arc_ecoli.tar.gz

Nov 7, 2024 - Supplementary Data for 'Vastly different energy landscapes of the membrane insertions of monomeric gasdermin D and A3'

Gzip Archive - 131.6 MB -

Replication Data for: Origin of the yield stress anomaly in L12 intermetallics unveiled with physically informed machine-learning potentials

Oct 8, 2024 - PN 3-10

Xu, Xiang, 2024, "Replication Data for: Origin of the yield stress anomaly in L12 intermetallics unveiled with physically informed machine-learning potentials", https://doi.org/10.18419/DARUS-4480, DaRUS, V1

Data for the manuscript "Origin of the yield stress anomaly in L12 intermetallics unveiled with physically-informed machine-learning potentials", https://doi.org/10.1016/j.actamat.2024.120423. This data set contains: 1) the utilized moment-tensor-potentials (MTP) and the corresponding training sets; 2) The atomistic structure of 2delta Kear-Wilsdor...

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