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Keyword Term: Molecular Dynamics Simulation

1 to 10 of 34 Results

Supplementary Information to "Linker-Cluster Cooperativity in Confinement of Proline- Functionalized Zr-Based Metal-Organic Frameworks and its Effect on the Organocatalytic Aldol Reaction" Apr 23, 2025 - SFB 1333 - Pluhackova Group, SimTech Kolin, Sofia; Pluhackova, Kristyna, 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"", https://doi.org/10.18419/DARUS-4834, DaRUS, V1 Files and structures for performing all-atom molecular dynamics simulations of UiO-67 and UiO-67-based structures filled with Methanol and reactant and product molecules.
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...
Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials" Feb 7, 2025 - SFB 1333 - Pluhackova Group, SimTech Kolin, Sofia; Marquardt, Moritz G.; Fläschner, Gotthold; Naumann, Stefan; Pluhackova, Kristyna, 2025, "Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"", https://doi.org/10.18419/DARUS-4740, DaRUS, V2 Files and structures for performing and analysing coarse-grained molecular dynamics simulations of solvent diffusion through nanoporous carbon materials.
Supplementary material for "The Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru-H Complex: Insights from Molecular Simulation and Neutron Scattering" Nov 4, 2024 - Institute of Thermodynamics and Thermal Process Engineering Högler, Marc; Hansen, Niels, 2024, "Supplementary material for "The Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru-H Complex: Insights from Molecular Simulation and Neutron Scattering"", https://doi.org/10.18419/DARUS-3584, DaRUS, V1, UNF:6:UUPJqhG8eXR2naMF0KSYGQ== [fileUNF] This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory mdp) are provided for bulk simulations of pure dioxane and formic acid as well as mixture of both in pore and bulk simulation. The pore simulation is divided into three steps, an energ...
Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining" Oct 16, 2024 - Holm group Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2024, "Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"", https://doi.org/10.18419/DARUS-4494, DaRUS, V1 Simulations and data analysis scripts for the publication "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining". Within gromacs-inputs, two types of GROMACS simulation scripts are provided: all-atom and united-atoms. In both cases, the system is a liquid propane bulk system. See the README file for...
Supplementary material for 'Probing Self-Diffusion of Guest Molecules in a Covalent Organic Framework: Simulation and Experiment' Jul 8, 2024 - Institute of Thermodynamics and Thermal Process Engineering Grunenberg, Lars; Kessler, Christopher; Teh, Tiong Wei; Schuldt, Robin; Heck, Fabian; Kästner, Johannes; Gross, Joachim; Hansen, Niels; Lotsch, Bettina V., 2024, "Supplementary material for 'Probing Self-Diffusion of Guest Molecules in a Covalent Organic Framework: Simulation and Experiment'", https://doi.org/10.18419/DARUS-3269, DaRUS, V1, UNF:6:vHsUiLwzEUUMiOsYM8xu+Q== [fileUNF] This dataset contains input files and results from Grand Canonical Monte Carlo (GCMC) adsorption simulation and Molecular Dynamics (MD) Simulation. All data is presented in a jupyter notebook and for a fast overview without executing the notebook also as PDF-file. Furthermore the dataset contains the modified cif files of COF PI-3, including partia...
Research Data Summary for: "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data" Jun 19, 2024 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences" Jaeger-Honz, Sabrina; Klein, Karsten; Schreiber, Falk, 2024, "Research Data Summary for: "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data"", https://doi.org/10.18419/DARUS-4251, DaRUS, V1 Here, we summarise available data and source code regarding the publication "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data". Abstract Computational methods such as molecular docking or molecular dynamics (MD) simulations have been developed to simulate and explore the interacti...
Research Data: "APL@voro—interactive visualization and analysis of cell membrane simulations" Jun 18, 2024 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences" Kern, Martin; Jaeger-Honz, Sabrina; Schreiber, Falk; Sommer, Björn, 2024, "Research Data: "APL@voro—interactive visualization and analysis of cell membrane simulations"", https://doi.org/10.18419/DARUS-4252, DaRUS, V1 Here, we summarise available data and source code regarding the publication "APL@voro—interactive visualization and analysis of cell membrane simulations". Abstract Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing...
Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis Jun 11, 2024 - Molecular Simulation Hansen, Niels; Markthaler, Daniel, 2024, "Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis", https://doi.org/10.18419/DARUS-4135, DaRUS, V1 This data set contains all relevant simulation input files (topologies, coordinates, simulation parameters), generated simulation output (final configurations, time series of collective variables) together with scripts used for set-up and analysis of the umbrella sampling and double decoupling simulations.
Replication Data for: Transferable Anisotropic Mie Potential Force Field for Alkanediols May 23, 2024 - Institute of Thermodynamics and Thermal Process Engineering Fleck, Maximilian; Darouich, Samir; Hansen, Niels; Gross, Joachim, 2024, "Replication Data for: Transferable Anisotropic Mie Potential Force Field for Alkanediols", https://doi.org/10.18419/DARUS-3824, DaRUS, V1 Supplementary material is provided for the Transferable Anisotropic Mie Potential Force Field for Alkanediols, including files for rerunning TURBOMOLE DFT calculations for 1,2-ethanediol and 1,3-propanediol. The dataset includes input files and results for the OCCO and OCCC torsion with various constrained H positions. Moreover, numerical values fo...

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

Apr 23, 2025 - SFB 1333 - Pluhackova Group, SimTech

Kolin, Sofia; Pluhackova, Kristyna, 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"", https://doi.org/10.18419/DARUS-4834, DaRUS, V1

Files and structures for performing all-atom molecular dynamics simulations of UiO-67 and UiO-67-based structures filled with Methanol and reactant and product molecules.

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...

Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"

Feb 7, 2025 - SFB 1333 - Pluhackova Group, SimTech

Kolin, Sofia; Marquardt, Moritz G.; Fläschner, Gotthold; Naumann, Stefan; Pluhackova, Kristyna, 2025, "Supplementary Information to "Molecular determinants of solvent nanoseparation by nanoporous carbon materials"", https://doi.org/10.18419/DARUS-4740, DaRUS, V2

Files and structures for performing and analysing coarse-grained molecular dynamics simulations of solvent diffusion through nanoporous carbon materials.

Supplementary material for "The Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru-H Complex: Insights from Molecular Simulation and Neutron Scattering"

Nov 4, 2024 - Institute of Thermodynamics and Thermal Process Engineering

Högler, Marc; Hansen, Niels, 2024, "Supplementary material for "The Effects of Surfaces and Confinement on Formic Acid Dehydrogenation Catalyzed by an Immobilized Ru-H Complex: Insights from Molecular Simulation and Neutron Scattering"", https://doi.org/10.18419/DARUS-3584, DaRUS, V1, UNF:6:UUPJqhG8eXR2naMF0KSYGQ== [fileUNF]

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory mdp) are provided for bulk simulations of pure dioxane and formic acid as well as mixture of both in pore and bulk simulation. The pore simulation is divided into three steps, an energ...

Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"

Oct 16, 2024 - Holm group

Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2024, "Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"", https://doi.org/10.18419/DARUS-4494, DaRUS, V1

Simulations and data analysis scripts for the publication "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining". Within gromacs-inputs, two types of GROMACS simulation scripts are provided: all-atom and united-atoms. In both cases, the system is a liquid propane bulk system. See the README file for...

Supplementary material for 'Probing Self-Diffusion of Guest Molecules in a Covalent Organic Framework: Simulation and Experiment'

Jul 8, 2024 - Institute of Thermodynamics and Thermal Process Engineering

Grunenberg, Lars; Kessler, Christopher; Teh, Tiong Wei; Schuldt, Robin; Heck, Fabian; Kästner, Johannes; Gross, Joachim; Hansen, Niels; Lotsch, Bettina V., 2024, "Supplementary material for 'Probing Self-Diffusion of Guest Molecules in a Covalent Organic Framework: Simulation and Experiment'", https://doi.org/10.18419/DARUS-3269, DaRUS, V1, UNF:6:vHsUiLwzEUUMiOsYM8xu+Q== [fileUNF]

This dataset contains input files and results from Grand Canonical Monte Carlo (GCMC) adsorption simulation and Molecular Dynamics (MD) Simulation. All data is presented in a jupyter notebook and for a fast overview without executing the notebook also as PDF-file. Furthermore the dataset contains the modified cif files of COF PI-3, including partia...

Research Data Summary for: "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data"

Jun 19, 2024 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences"

Jaeger-Honz, Sabrina; Klein, Karsten; Schreiber, Falk, 2024, "Research Data Summary for: "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data"", https://doi.org/10.18419/DARUS-4251, DaRUS, V1

Here, we summarise available data and source code regarding the publication "Systematic analysis, aggregation and visualisation of interaction fingerprints for molecular dynamics simulation data". Abstract Computational methods such as molecular docking or molecular dynamics (MD) simulations have been developed to simulate and explore the interacti...

Research Data: "APL@voro—interactive visualization and analysis of cell membrane simulations"

Jun 18, 2024 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences"

Kern, Martin; Jaeger-Honz, Sabrina; Schreiber, Falk; Sommer, Björn, 2024, "Research Data: "APL@voro—interactive visualization and analysis of cell membrane simulations"", https://doi.org/10.18419/DARUS-4252, DaRUS, V1

Here, we summarise available data and source code regarding the publication "APL@voro—interactive visualization and analysis of cell membrane simulations". Abstract Molecular dynamics (MD) simulations of cell membranes allow for a better understanding of complex processes such as changing membrane dynamics, lipid rafts and the incorporation/passing...

Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis

Jun 11, 2024 - Molecular Simulation

Hansen, Niels; Markthaler, Daniel, 2024, "Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis", https://doi.org/10.18419/DARUS-4135, DaRUS, V1

This data set contains all relevant simulation input files (topologies, coordinates, simulation parameters), generated simulation output (final configurations, time series of collective variables) together with scripts used for set-up and analysis of the umbrella sampling and double decoupling simulations.

Replication Data for: Transferable Anisotropic Mie Potential Force Field for Alkanediols

May 23, 2024 - Institute of Thermodynamics and Thermal Process Engineering

Fleck, Maximilian; Darouich, Samir; Hansen, Niels; Gross, Joachim, 2024, "Replication Data for: Transferable Anisotropic Mie Potential Force Field for Alkanediols", https://doi.org/10.18419/DARUS-3824, DaRUS, V1

Supplementary material is provided for the Transferable Anisotropic Mie Potential Force Field for Alkanediols, including files for rerunning TURBOMOLE DFT calculations for 1,2-ethanediol and 1,3-propanediol. The dataset includes input files and results for the OCCO and OCCC torsion with various constrained H positions. Moreover, numerical values fo...

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