PN 3

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

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331 to 340 of 1,130 Results

topol.top Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations Unknown - 2.2 KB - MD5: 2bea99dd255d2f21267b525efcd8bc0e
topol.top Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations Unknown - 2.2 KB - MD5: ee13d279581149af78e2f02322bfe0e4
topol.top Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations Unknown - 2.5 KB - MD5: 19003ec06798e0246b011672fb81fac3
Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF" Sep 9, 2025 - PN 3-11 Pluhackova, Kristyna, 2025, "Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"", https://doi.org/10.18419/DARUS-5324, DaRUS, V1 Simulation files, molecular structures and trajectories tetrameric GlpF wild type and M4C mutant. in the latter, 4 cysteine residues in the transmembrane helix bundle of GlpF, in detail C11, C28, C80, and C99 are replaced by glycines. The data underlays our publication on the role of those 4 cysteine residues for stability of membrane inserted tetr...
charmm36-jul2017.tar.gz Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF" Gzip Archive - 602.5 KB - MD5: 16e479102c1163f7568dbe5333c35863
M4C_tetra.tar.gz Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF" Gzip Archive - 3.4 GB - MD5: 20bb7ba8f2e6715f40dc5a012f44cf93 simulation files and results of the mutated tetrameric GlpF protein
wt_tetra.tar.gz Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF" Gzip Archive - 3.4 GB - MD5: 6b2ec643c05b804388672956c6496c46 simulation files and results of the wild-type tetrameric GlpF
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.

topol.top

Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations

Unknown - 2.2 KB -

topol.top

Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations

Unknown - 2.2 KB -

topol.top

Nov 25, 2025 - Supplementary Data for: Static Dielectric Profiles and Coarse-graining Approaches for Water in Graphene Slit Pores: The Crucial Influence of Boundary Conditions in Simulations

Unknown - 2.5 KB -

Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"

Sep 9, 2025 - PN 3-11

Pluhackova, Kristyna, 2025, "Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"", https://doi.org/10.18419/DARUS-5324, DaRUS, V1

Simulation files, molecular structures and trajectories tetrameric GlpF wild type and M4C mutant. in the latter, 4 cysteine residues in the transmembrane helix bundle of GlpF, in detail C11, C28, C80, and C99 are replaced by glycines. The data underlays our publication on the role of those 4 cysteine residues for stability of membrane inserted tetr...

charmm36-jul2017.tar.gz

Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"

Gzip Archive - 602.5 KB -

M4C_tetra.tar.gz

Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"

Gzip Archive - 3.4 GB -

simulation files and results of the mutated tetrameric GlpF protein

wt_tetra.tar.gz

Sep 9, 2025 - Supplementary Data to: "Cysteine-mediated structural stabilization of the tetrameric GlpF"

Gzip Archive - 3.4 GB -

simulation files and results of the wild-type tetrameric GlpF

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.

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