Subject: Chemistry
Keyword Term: Molecular Dynamics Simulation
Subject: Computer and Information Science
1 to 10 of 10 Results
Oct 11, 2023 - NMR insights into nanoconfined water using the surface exchange model
Gravelle, Simon, 2023, "Molecular simulation scripts for slit nanopores with tunable hydrophilicity", https://doi.org/10.18419/darus-3732, DaRUS, V1
GROMACS molecular simulation input files for slit nanopores filled with liquid water. Initial configuration can be generated using the Python script build_system.py. Use the bash script run_gmx.sh to run GROMACS. See the README.md file. |
Sep 21, 2023 - Molecular Simulation
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... |
Mar 9, 2023 - NMR investigation of water confined by salt interface
Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for slit nanopores", https://doi.org/10.18419/darus-3180, DaRUS, V1
GROMACS molecular simulation input files for slit nanopores made of NaCl and Na2SO4 solid walls, and filled with respectively NaCl and Na2SO4 solutions. Initial configuration with a given salt concentration can be generated using the Python script ConfigurationGenerator.py, and s... |
Mar 8, 2023 - NMR investigation of water confined by salt interface
Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/darus-3179, DaRUS, V1
GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash s... |
Mar 25, 2022 - Thin Film Water on NaCl(100)
Gravelle, Simon, 2022, "Movies of thin film water on rough NaCl surface", https://doi.org/10.18419/darus-2770, DaRUS, V1
Videos showing water molecules at a rough sodium chloride solid surface for different roughness and different water chemical potential. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https... |
Mar 25, 2022 - Thin Film Water on NaCl(100)
Gravelle, Simon, 2022, "Molecular simulation scripts for thin film water on NaCl surface", https://doi.org/10.18419/darus-2726, DaRUS, V1
LAMMPS and GROMACS molecular simulation input files. The system consists of thin film water confined in a 7 nm NaCl slit pore, and can be generated using the Python scripts in SystemGeneration. The simulation is either equilibrium molecular dynamics (EMD), non equilibrium molecul... |
Mar 25, 2022 - Thin Film Water on NaCl(100)
Gravelle, Simon, 2022, "Movies of thin film water on NaCl(100) surface", https://doi.org/10.18419/darus-2697, DaRUS, V1
Videos showing water molecules at a sodium chloride (NaCl) solid surface for different water content. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https://doi.org/10.1021/acs.jpcb.1c0530... |
Mar 9, 2022 - Molecular Simulation
Kraus, Hamzeh; Hansen, Niels, 2022, "Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'", https://doi.org/10.18419/darus-2154, DaRUS, V1
This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for all simulations conducted within the paper. The simulation is divided into three steps, an energy-minimizati... |
Kraus, Hamzeh; Rybka, Julia; Hansen, Niels, 2022, "Supplementary material for 'Computational study of confinement effects in molecular heterogeneous catalysis'", https://doi.org/10.18419/darus-488, DaRUS, V1
This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology and simulation parameter-files are provided for six simulations - two pore sizes of 9nm and 6nm, each with simulations of pure substrate, pure product and a... |
Kraus, Hamzeh; Hansen, Niels, 2021, "Supplementary material for 'Confinement Effects for Efficient Macrocyclization Reactions with Supported Cationic Molybdenum Imido Alkylidene N‑Heterocyclic Carbene Complexes'", https://doi.org/10.18419/darus-1752, DaRUS, V1
This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files (directory Mdp) are provided for four simulations - a 2.5 nm pore with one catalyst molecule, a 2.5 nm pore with two catalyst... |
