Molecular Simulation

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Publication Year: 2022

1 to 10 of 214 Results

Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Mar 9, 2022 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...
298_bcd_1_ben_1_biased_bound.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 212.9 KB - MD5: b9e5417ddd7c9affc2feebe009cfccf9 Cartesian coordinates of the biased free energy simulation in the bound state with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_ben_1_biased_unbound.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 203.0 KB - MD5: 330bbb94560508ce8953d0dec6fa9ff6 Cartesian coordinates of the biased free energy simulation in the unbound state with 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_ben_1_colvar.txt Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Plain Text - 494.9 MB - MD5: f2bab1699d0266c5ff916d7b5a783de1 Plumed output file of a 1 mus simulation at 298 K with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules in txt format.
298_bcd_1_ben_1_unbiased.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 212.9 KB - MD5: c001f58bb63403c1a9e53d9c99951549 Cartesian coordinates of the unbiased free energy simulation state with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_pnp_1_biased_bound_o1.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 213.2 KB - MD5: 247a4092c6395c4b958c36cc6b8da795 Cartesian coordinates of the biased free energy simulation in the bound state in orientation 1 with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_pnp_1_biased_bound_o2.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 213.2 KB - MD5: e305fe61da4d374b7a06f579f8cc148d Cartesian coordinates of the biased free energy simulation in the bound state in orientation 2 with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_pnp_1_biased_unbound.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 203.3 KB - MD5: 657a9d28e8ba36a1d7ef07756493f934 Cartesian coordinates of the biased free energy simulation in the unbound state with 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.
298_bcd_1_pnp_1_colvar.txt Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Plain Text - 494.9 MB - MD5: e8358ac33fe8e19152ca7be4899cbb17 Plumed output file of a 1 mus simulation at 298 K with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules in txt format.
298_bcd_1_pnp_1_unbiased.gro Mar 9, 2022 - Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' Unknown - 213.1 KB - MD5: 13c60536c5e9f134cb63d1dd00e70cbc Cartesian coordinates of the unbiased free energy simulation state with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.

Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica'

Mar 9, 2022

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...

298_bcd_1_ben_1_biased_bound.gro

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

Unknown - 212.9 KB -

Cartesian coordinates of the biased free energy simulation in the bound state with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_ben_1_biased_unbound.gro

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

Unknown - 203.0 KB -

Cartesian coordinates of the biased free energy simulation in the unbound state with 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_ben_1_colvar.txt

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

Plain Text - 494.9 MB -

Plumed output file of a 1 mus simulation at 298 K with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules in txt format.

298_bcd_1_ben_1_unbiased.gro

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

Unknown - 212.9 KB -

Cartesian coordinates of the unbiased free energy simulation state with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_pnp_1_biased_bound_o1.gro

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

Unknown - 213.2 KB -

Cartesian coordinates of the biased free energy simulation in the bound state in orientation 1 with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_pnp_1_biased_bound_o2.gro

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

Unknown - 213.2 KB -

Cartesian coordinates of the biased free energy simulation in the bound state in orientation 2 with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_pnp_1_biased_unbound.gro

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

Unknown - 203.3 KB -

Cartesian coordinates of the biased free energy simulation in the unbound state with 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.

298_bcd_1_pnp_1_colvar.txt

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

Plain Text - 494.9 MB -

Plumed output file of a 1 mus simulation at 298 K with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules in txt format.

298_bcd_1_pnp_1_unbiased.gro

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

Unknown - 213.1 KB -

Cartesian coordinates of the unbiased free energy simulation state with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules simulated at 298 K in .gro format.

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