Molecular Simulation

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File Type: Code

1 to 10 of 10 Results

generate_pore.ipynb Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Jupyter Notebook - 15.9 KB - MD5: f93613c78c2c28c6075480d22f0527aa notebook to generate the pore which was used for the simulations. The porems package is needed. Please set the environment with the yaml file in the data set
open_thermoml.ipynb Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Jupyter Notebook - 4.8 KB - MD5: 631f432a3e6cef1ed60524ad6e90db4c Notebook to read the thermoml file with openff. Please set up first the environment with the yaml file
read_exp_data.ipynb Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Jupyter Notebook - 56.0 KB - MD5: 5415e023aab0f80edfcc76533cce0576 notebook to read the yaml files with the experimental data which would be used for comparison with simulation data
results_notebook.ipynb Sep 21, 2023 - Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Jupyter Notebook - 20.8 KB - MD5: b37712161dac5c4955ad654c64cb0b77 Example notebook to display results and plots of the publication. Please run "conda env create -f environment.yml" with the environment file in the data set to install all necessary packages for the example notebook
cluster.sh Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Shell Script - 307 B - MD5: 7e56a792ff215d1960621df8c6848467 Exemplary shell file for job submission on clusters to be used in combination with the PoreSim python package.
poreana.ipynb Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Jupyter Notebook - 5.5 KB - MD5: 8bd4b43a939399d2927860a30a3d8f42 Jupyter-Notebook for pore trajectory analysis using the PoreAna python package.
porems.ipynb Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Jupyter Notebook - 20.5 KB - MD5: 1e14096ab35db6cc295c68b281f32363 Jupyter-Notebook for pore system generation using the PoreMS python package.
poresim.ipynb Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Jupyter Notebook - 6.6 KB - MD5: 87fd7d7600725ed3879b7c1d690281ce Jupyter-Notebook for pore simulation preparation for GROMACS using the PoreSim python package.
cata.ipynb Feb 10, 2021 - Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions' Jupyter Notebook - 21.5 KB - MD5: ec45e060abb9eb3b078f12c7480b6230 Jupyter Notebook for generating a cylindrical catalytic mesopore model.
rplc.ipynb Feb 10, 2021 - Supplementary material for 'PoreMS: A software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions' Jupyter Notebook - 41.5 KB - MD5: a05a5d527a13a5cee785965dcd8f4079 Jupyter Notebook for generating a cylindrical RPLC mesopore model.

generate_pore.ipynb

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

Jupyter Notebook - 15.9 KB -

notebook to generate the pore which was used for the simulations. The porems package is needed. Please set the environment with the yaml file in the data set

open_thermoml.ipynb

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

Jupyter Notebook - 4.8 KB -

Notebook to read the thermoml file with openff. Please set up first the environment with the yaml file

read_exp_data.ipynb

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

Jupyter Notebook - 56.0 KB -

notebook to read the yaml files with the experimental data which would be used for comparison with simulation data

results_notebook.ipynb

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

Jupyter Notebook - 20.8 KB -

Example notebook to display results and plots of the publication. Please run "conda env create -f environment.yml" with the environment file in the data set to install all necessary packages for the example notebook

cluster.sh

Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'

Shell Script - 307 B -

Exemplary shell file for job submission on clusters to be used in combination with the PoreSim python package.

poreana.ipynb

Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'

Jupyter Notebook - 5.5 KB -

Jupyter-Notebook for pore trajectory analysis using the PoreAna python package.

porems.ipynb

Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'

Jupyter Notebook - 20.5 KB -

Jupyter-Notebook for pore system generation using the PoreMS python package.