SFB 1333 - Pluhackova Group, SimTech

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1 to 10 of 10 Results

simulation_files.tar.gz Apr 23, 2025 - Supplementary Information to "Linker-Cluster Cooperativity in Confinement of Proline- Functionalized Zr-Based Metal-Organic Frameworks and its Effect on the Organocatalytic Aldol Reaction" Gzip Archive - 8.5 MB - MD5: fbb38a174be35650df9f4d7a0ff9585a GROMACS simulation files (topologies, index, mdp and itp files) as well as structures of the individual systems studied.
analysis.tar.gz Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Gzip Archive - 2.4 MB - MD5: 3d7fda4ab58d38397eab99173e66054b Analysis scripts and jupyter notebooks
itp_files.tar.gz Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Gzip Archive - 15.3 MB - MD5: 83ce7b9c0983db969665945ba94c49ee itp files common to multiple simulations. For completeness this folder also includes the files martini_v.3.0.0.itp and martini_v3.0.0_solvents.itp from the standard martini repository https://github.com/marrink-lab/martini-forcefields/tree/main/martini_forcefields/regular/v3.0.0/gmx_files Please cite PCT Souza, et al., Nat. Methods, 2021. DOI: 10....
markov_model.tar.gz Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Gzip Archive - 3.7 MB - MD5: f12cd83220d5a372c0c3e5adcbfb8edd jupyter notebook and input files for the developed markov model describing the first passage times through a cubic material
material_builder.tar.gz Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Gzip Archive - 15.4 MB - MD5: 54a5d1fe38249b8b434c3ee00bfbf4f4
simulation_files.tar.gz Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Gzip Archive - 152.5 MB - MD5: 59e52ee52dfc4c9c93fecf12a1d73950 GROMACS simulation files (topologies, index and mdp files) as well as structures of the individual systems studied sorted in 3 categories- solvent systems, cubic systems and hexagonal systems
AQP1.tar.gz Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Gzip Archive - 21.3 MB - MD5: d07962502998949580f947c62f1ef616 Simulation and analysis files of tetrameric AQP1 embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested...
AQPZ.tar.gz Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Gzip Archive - 15.8 MB - MD5: f48975c095655931b44dea6581c0ee76 Simulation and analysis files of tetrameric AQPZ embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested...
charmm36-jul2017.ff.tar.gz Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Gzip Archive - 600.2 KB - MD5: 17188dcad81e662ab1df296a90650f97 GROMACS simulation files for CHARMM36m including all special atomtypes from this project (also for CNTs).
CNT.tar.gz Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Gzip Archive - 24.4 MB - MD5: 2fa8beda83c9b939fbefbcb4bde6e374 Simulation and analysis files of four single layered narrow carbon nanotube porins (16 repetition-long) embedded in a DLPC membrane. All-atom simulation using CHARMM36m force field. Structures after 500ns at 289K, 299K, 309K, and 319K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corre...

simulation_files.tar.gz

Apr 23, 2025 - Supplementary Information to "Linker-Cluster Cooperativity in Confinement of Proline- Functionalized Zr-Based Metal-Organic Frameworks and its Effect on the Organocatalytic Aldol Reaction"

Gzip Archive - 8.5 MB -

GROMACS simulation files (topologies, index, mdp and itp files) as well as structures of the individual systems studied.

analysis.tar.gz

Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Gzip Archive - 2.4 MB -

Analysis scripts and jupyter notebooks

itp_files.tar.gz

Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Gzip Archive - 15.3 MB -

itp files common to multiple simulations. For completeness this folder also includes the files martini_v.3.0.0.itp and martini_v3.0.0_solvents.itp from the standard martini repository https://github.com/marrink-lab/martini-forcefields/tree/main/martini_forcefields/regular/v3.0.0/gmx_files Please cite PCT Souza, et al., Nat. Methods, 2021. DOI: 10....

markov_model.tar.gz

Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Gzip Archive - 3.7 MB -

jupyter notebook and input files for the developed markov model describing the first passage times through a cubic material

material_builder.tar.gz

Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Gzip Archive - 15.4 MB -

simulation_files.tar.gz

Feb 7, 2025 - Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Gzip Archive - 152.5 MB -

GROMACS simulation files (topologies, index and mdp files) as well as structures of the individual systems studied sorted in 3 categories- solvent systems, cubic systems and hexagonal systems

AQP1.tar.gz

Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Gzip Archive - 21.3 MB -

Simulation and analysis files of tetrameric AQP1 embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested...

AQPZ.tar.gz

Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Gzip Archive - 15.8 MB -

Simulation and analysis files of tetrameric AQPZ embedded in E. coli PLE membrane model. All-atom simulation using CHARMM36m force field. Structures after 500ns at 277K, 289K, 296K and 309K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corresponding directories. The workflow is tested...

charmm36-jul2017.ff.tar.gz

Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Gzip Archive - 600.2 KB -

GROMACS simulation files for CHARMM36m including all special atomtypes from this project (also for CNTs).

CNT.tar.gz

Jun 30, 2023 - Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Gzip Archive - 24.4 MB -

Simulation and analysis files of four single layered narrow carbon nanotube porins (16 repetition-long) embedded in a DLPC membrane. All-atom simulation using CHARMM36m force field. Structures after 500ns at 289K, 299K, 309K, and 319K are also included. Guides how to run and analyse the simulations are included in the workflow.sh files in the corre...

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