Molecular Simulation

Dataverse concerning Molecular simulation studies.

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391 to 400 of 578 Results

nvt_biased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 2.9 KB - MD5: 043ce49c734a10e14a4edc5853c8297f Simulation parameter file of the NVT equilibration step of the biased free energy simulation in .mdp format.
nvt_pore.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 1.7 KB - MD5: e5af588b09739b77aaeb9c2000c2a426 Simulation parameter file of the NVT equilibration step of the pore simulation in .mdp format.
nvt_unbiased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 1.4 KB - MD5: 3883f82c9f8da2c17f6e0788f7fadfcd Simulation parameter file of the NVT equilibration step of the unbiased free energy simulation in .mdp format.
pnp_1.top Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 1010 B - MD5: 5a066edd14f86419ae3a8f5138abea68 Main topology file of the free energy simulation with 1 p-nitrophenol molecule in 1000 water molecules in .top format.
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.
pore_clear.pms Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' TGIF File - 4.4 MB - MD5: 50481c8e23a696996e6ff51afbc5fc76 PoreMS object file of the pore without functionalization in pickle format protocol version 3.
pore_clear_slit.pms Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' TGIF File - 6.5 MB - MD5: 7677a08974492190a23ad857cd8856e7 PoreMS object file of the slit-pore without functionalization in pickle format protocol version 3.
pore_huq_11.pms Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' TGIF File - 4.9 MB - MD5: 10ee44138ae50eeb0953cd448cfac005 PoreMS object file of the pore with 11 beta-CD molecules attached to the surface using the Huq linker in pickle format protocol version 3.
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.

nvt_biased.mdp

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

Unknown - 2.9 KB -

Simulation parameter file of the NVT equilibration step of the biased free energy simulation in .mdp format.

nvt_pore.mdp

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

Unknown - 1.7 KB -

Simulation parameter file of the NVT equilibration step of the pore simulation in .mdp format.

nvt_unbiased.mdp

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

Unknown - 1.4 KB -

Simulation parameter file of the NVT equilibration step of the unbiased free energy simulation in .mdp format.

pnp_1.top

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

Unknown - 1010 B -

Main topology file of the free energy simulation with 1 p-nitrophenol molecule in 1000 water molecules in .top format.

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.

pore_clear.pms

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

TGIF File - 4.4 MB -

PoreMS object file of the pore without functionalization in pickle format protocol version 3.

pore_clear_slit.pms

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

TGIF File - 6.5 MB -

PoreMS object file of the slit-pore without functionalization in pickle format protocol version 3.

pore_huq_11.pms

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

TGIF File - 4.9 MB -

PoreMS object file of the pore with 11 beta-CD molecules attached to the surface using the Huq linker in pickle format protocol version 3.

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.

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 -

Jupyter-Notebook for pore simulation preparation for GROMACS using the PoreSim python package.

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