Molecular Simulation

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1 to 10 of 587 Results

Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis Jun 11, 2024 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 dou...
TerpenesCycl_NCOMMS_MDSim_SI.tar.gz Jun 11, 2024 - Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis Gzip Archive - 544.8 MB - MD5: 23ce24f6e0dffec44024721b86a5aec6 contains GROMACS topologies, coordinate files, software, and a prototypical double decoupling workflow for the ambroxide-beta cyclodextrin complex
Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Sep 21, 2023 Kraus, Hamzeh; Högler, Marc; Hansen, Niels, 2023, "Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'", https://doi.org/10.18419/darus-3067, DaRUS, V1 This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for bulk phase simulations as well as for pore simulations with 14 different compounds. The pore simulations are...
1-butanol.gro Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 740 B - MD5: f96c5d4888d27a901d7a58b9175cabdc Cartesian coordinates of a single 1-butanol molecule in .gro format.
1-butanol.top Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 9.1 KB - MD5: cc98395393960b384e3b32d3d4469dc5 Topology file of a 1-butanol molecule in .top format.
1-propanol.gro Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 605 B - MD5: 2efbf3f74fb753c88848b26f90039c28 Cartesian coordinates of a single 1-propanol molecule in .gro format.
1-propanol.top Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 6.9 KB - MD5: 68299bf382750177b89434aa9134df8e Topology file of a 1-propanol molecule in .top format.
benzene.gro Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 605 B - MD5: b08077660fab51bfdce1a2a107f4aed8 Cartesian coordinates of a single benzene molecule in .gro format.
benzene.top Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Unknown - 7.3 KB - MD5: e1c7f3f7f8fbb2432a08a47ce6724c60 Topology file of a benzene molecule in .top format.
box_rectangular_1-butanol_density.h5 Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Hierarchical Data Format - 16.9 KB - MD5: 560023d37a71544e4faeef24283c3216 Center of mass density profiles of 1-butanol from a simulation of an rectangular box with pure 1-butanol simulated at 295K in HDF5 format.

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

Jun 11, 2024

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 dou...

TerpenesCycl_NCOMMS_MDSim_SI.tar.gz

Jun 11, 2024 - Replication Data for: Biocatalytic stereocontrolled head-to-tail cyclizations of unbiased terpenes as a tool in chemoenzymatic synthesis

Gzip Archive - 544.8 MB -

contains GROMACS topologies, coordinate files, software, and a prototypical double decoupling workflow for the ambroxide-beta cyclodextrin complex

Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Sep 21, 2023

Kraus, Hamzeh; Högler, Marc; Hansen, Niels, 2023, "Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'", https://doi.org/10.18419/darus-3067, DaRUS, V1

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for bulk phase simulations as well as for pore simulations with 14 different compounds. The pore simulations are...

1-butanol.gro

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 740 B -

Cartesian coordinates of a single 1-butanol molecule in .gro format.

1-butanol.top

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 9.1 KB -

Topology file of a 1-butanol molecule in .top format.

1-propanol.gro

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 605 B -

Cartesian coordinates of a single 1-propanol molecule in .gro format.

1-propanol.top

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 6.9 KB -

Topology file of a 1-propanol molecule in .top format.

benzene.gro

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 605 B -

Cartesian coordinates of a single benzene molecule in .gro format.

benzene.top

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Unknown - 7.3 KB -

Topology file of a benzene molecule in .top format.

box_rectangular_1-butanol_density.h5

Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Hierarchical Data Format - 16.9 KB -

Center of mass density profiles of 1-butanol from a simulation of an rectangular box with pure 1-butanol simulated at 295K in HDF5 format.

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