Molecular Simulation

Dataverse concerning Molecular simulation studies.

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381 to 390 of 578 Results

gcd_trofy.top Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 105.2 KB - MD5: 08e80ddedfba76a1e0aa48c606c76ad8 Topology file of a gamma-CD molecule with a Trofymchuk surface linker in .top format.
grid.itp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' application/vnd.shana.informed.formtemplate - 1.6 KB - MD5: b761c8afe21af2f07235ff893ccdf671 Topology file of all used grid molecules of the pore system in .itp format.
huq_350_11_1mus_7.5ns-p-s.mp4 Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' MPEG-4 Video - 1.0 GB - MD5: 82910b4c8dcbbf5c34ee5734582059ee MD Simulation trajectory of 1 mus simulated at 350 K of a Pore with 11 beta-CD molecules attached to the surface using the Huq linker with 30 p-nitrophenol molecules in water. Hereby one video second corresponds to 7.5 ns.
min_biased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 2.0 KB - MD5: 5a1fd4cfca51def1f7aa6c3d6f99af51 Simulation parameter file of the energy-minimization step of the biased free energy simulation in .mdp format.
min_pore.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 988 B - MD5: a1368b8478281f24c6626e425164d46d Simulation parameter file of the energy-minimization step of the pore simulation in .mdp format.
min_unbiased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 848 B - MD5: 55145d59b6e51dc9fabcbfdf0f76a5e4 Simulation parameter file of the energy-minimization step of the unbiased free energy simulation in .mdp format.
nitrophenol.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 779 B - MD5: 47c5b6d5d53c9a8a87e2dab9c41ea9fa Cartesian coordinates of a single p-nitrophenol molecule in .gro format.
nitrophenol.top Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 9.1 KB - MD5: 48ffb6a0a4c1781278a4a7e1b181f325 Topology file of a p-nitrophenol molecule in .top format.
npt_biased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 3.0 KB - MD5: 5ad6fde952d089679061163ef799f63b Simulation parameter file of the NpT equilibration step of the biased free energy simulation in .mdp format.
npt_unbiased.mdp Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 1.5 KB - MD5: 28a8d806cac89bb969cbfcc013a53bcf Simulation parameter file of the NpT equilibration step of the unbiased free energy simulation in .mdp format.

gcd_trofy.top

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

Unknown - 105.2 KB -

Topology file of a gamma-CD molecule with a Trofymchuk surface linker in .top format.

grid.itp

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

application/vnd.shana.informed.formtemplate - 1.6 KB -

Topology file of all used grid molecules of the pore system in .itp format.

huq_350_11_1mus_7.5ns-p-s.mp4

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

MPEG-4 Video - 1.0 GB -

MD Simulation trajectory of 1 mus simulated at 350 K of a Pore with 11 beta-CD molecules attached to the surface using the Huq linker with 30 p-nitrophenol molecules in water. Hereby one video second corresponds to 7.5 ns.

min_biased.mdp

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

Unknown - 2.0 KB -

Simulation parameter file of the energy-minimization step of the biased free energy simulation in .mdp format.

min_pore.mdp

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

Unknown - 988 B -

Simulation parameter file of the energy-minimization step of the pore simulation in .mdp format.

min_unbiased.mdp

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

Unknown - 848 B -

Simulation parameter file of the energy-minimization step of the unbiased free energy simulation in .mdp format.

nitrophenol.gro

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

Unknown - 779 B -

Cartesian coordinates of a single p-nitrophenol molecule in .gro format.

nitrophenol.top

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

Unknown - 9.1 KB -

Topology file of a p-nitrophenol molecule in .top format.

npt_biased.mdp

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

Unknown - 3.0 KB -

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

npt_unbiased.mdp

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

Unknown - 1.5 KB -

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

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