Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' (doi:10.18419/darus-2154)

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

doi:10.18419/darus-2154

DaRUS

2022-03-09

1

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

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

doi:10.18419/darus-2154

Kraus, Hamzeh (University of Stuttgart)

Hansen, Niels (University of Stuttgart)

358283783 - SFB 1333

DaRUS

Kraus, Hamzeh

Hansen, Niels

Kraus, Hamzeh

2021-09-21

https://doi.org/10.18419/darus-2154

Chemistry, Computer and Information Science, Molecular Dynamics Simulation, Adsorption, Cyclodextrins, Mesoporous Silica

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-minimization, an NVT equilibration, and an NVT production simulation run. Provided structure files are of an already equilibrated system. Object files are supplied which can be used to load the generated pores into PoreMS for later alteration and analysis. Additionally, short movies can be viewed for the different systems.

Kraus, H. & Hansen, N. (2022): An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica. Adsorption.

10.1007/s10450-022-00356-w

Kraus, H. & Hansen, N. (2022): An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica. Adsorption.

Label:

cluster.sh

Text:

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

text/x-sh

Label:

poreana.ipynb

Text:

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

application/x-ipynb+json

Label:

porems.ipynb

Text:

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

application/x-ipynb+json

Label:

poresim.ipynb

Text:

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

application/x-ipynb+json

Label:

pore_clear.pms

Text:

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

application/x-tgif

Label:

pore_system_clear.pms

Text:

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

application/x-tgif

Label:

pore_clear_slit.pms

Text:

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

application/x-tgif

Label:

pore_system_clear_slit.pms

Text:

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

application/x-tgif

Label:

pore_huq_11.pms

Text:

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.

application/x-tgif

Label:

pore_system_huq_11.pms

Text:

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

application/x-tgif

Label:

pore_system_trofy_05.pms

Text:

PoreMS object file of the pore system with 5 beta-CD molecules attached to the surface using the Trofymchuk linker in pickle format protocol version 3.

application/x-tgif

Label:

pore_trofy_05.pms

Text:

PoreMS object file of the pore with 5 beta-CD molecules attached to the surface using the Trofymchuk linker in pickle format protocol version 3.

application/x-tgif

Label:

pore_system_trofy_11.pms

Text:

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

application/x-tgif

Label:

pore_trofy_11.pms

Text:

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

application/x-tgif

Label:

pore_system_trofy_11_slit.pms

Text:

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

application/x-tgif

Label:

pore_trofy_11_slit.pms

Text:

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

application/x-tgif

Label:

298_bcd_1_ben_1_colvar.txt

Text:

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.

text/plain

Label:

298_bcd_1_pnp_1_colvar.txt

Text:

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.

text/plain

Label:

350_bcd_1_ben_1_colvar.txt

Text:

Plumed output file of a 1 mus simulation at 350 K with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules in txt format.

text/plain

Label:

350_bcd_1_pnp_1_colvar.txt

Text:

Plumed output file of a 1 mus simulation at 350 K with 1 beta-CD molecule and 1 p-nitrophenol molecule in 1000 water molecules in txt format.

text/plain

Label:

bcd_1_ben_1_plumed.dat

Text:

Plumed data file of the simulation box with 1 beta-CD molecule and 1 benzene molecule with 1000 water molecules in plumed format.

text/x-fixed-field

Label:

bcd_1_pnp_1_plumed.dat

Text:

Plumed data file of the simulation box with 1 beta-CD molecule and 1 p-nitrophenol molecule with 1000 water molecules in plumed format.

text/x-fixed-field

Label:

min_biased.mdp

Text:

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

application/octet-stream

Label:

npt_biased.mdp

Text:

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

application/octet-stream

Label:

nvt_biased.mdp

Text:

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

application/octet-stream

Label:

run_biased.mdp

Text:

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

application/octet-stream

Label:

min_pore.mdp

Text:

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

application/octet-stream

Label:

nvt_pore.mdp

Text:

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

application/octet-stream

Label:

run_pore.mdp

Text:

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

application/octet-stream

Label:

min_unbiased.mdp

Text:

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

application/octet-stream

Label:

npt_unbiased.mdp

Text:

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

application/octet-stream

Label:

nvt_unbiased.mdp

Text:

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

application/octet-stream

Label:

run_unbiased.mdp

Text:

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

application/octet-stream

Label:

298_bcd_1_ben_1_biased_bound.gro

Text:

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.

application/octet-stream

Label:

298_bcd_1_ben_1_biased_unbound.gro

Text:

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.

application/octet-stream

Label:

298_bcd_1_pnp_1_biased_bound_o1.gro

Text:

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.

application/octet-stream

Label:

298_bcd_1_pnp_1_biased_bound_o2.gro

Text:

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.

application/octet-stream

Label:

298_bcd_1_pnp_1_biased_unbound.gro

Text:

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.

application/octet-stream

Label:

350_bcd_1_ben_1_biased_bound.gro

Text:

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 350 K in .gro format.

application/octet-stream

Label:

350_bcd_1_ben_1_biased_unbound.gro

Text:

Cartesian coordinates of the biased free energy simulation in the unbound state with 1 benzene molecule in 1000 water molecules simulated at 350 K in .gro format.

application/octet-stream

Label:

350_bcd_1_pnp_1_biased_bound_o1.gro

Text:

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 350 K in .gro format.

application/octet-stream

Label:

350_bcd_1_pnp_1_biased_bound_o2.gro

Text:

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 350 K in .gro format.

application/octet-stream

Label:

350_bcd_1_pnp_1_biased_unbound.gro

Text:

Cartesian coordinates of the biased free energy simulation in the unbound state with 1 p-nitrophenol molecule in 1000 water molecules simulated at 350 K in .gro format.

application/octet-stream

Label:

acd.gro

Text:

Cartesian coordinates of an alpha-CD molecule in .gro format.

application/octet-stream

Label:

acd_huq.gro

application/octet-stream

Label:

acd_trofy.gro

Text:

Cartesian coordinates of an alpha-CD molecule with a Trofymchuk surface linker in .gro format.

application/octet-stream

Label:

bcd.gro

Text:

Cartesian coordinates of a beta-CD molecule in .gro format.

application/octet-stream

Label:

bcd_huq.gro

Text:

Cartesian coordinates of a beta-CD molecule with a Huq surface linker in .gro format.

application/octet-stream

Label:

bcd_trofy.gro

Text:

Cartesian coordinates of a beta-CD molecule with a Trofymchuk surface linker in .gro format.

application/octet-stream

Label:

gcd.gro

Text:

Cartesian coordinates of a gamma-CD molecule in .gro format.

application/octet-stream

Label:

gcd_huq.gro

Text:

Cartesian coordinates of a gamma-CD molecule with a Huq surface linker in .gro format.

application/octet-stream

Label:

gcd_trofy.gro

Text:

Cartesian coordinates of a gamma-CD molecule with a Trofymchuk surface linker in .gro format.

application/octet-stream

Label:

298_ben_10.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_ben_20.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_ben_60.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_05_ben_20.ndx

Text:

Index file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_05_ben_40.ndx

Text:

Index file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 40 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_05_ben_60.ndx

Text:

Index file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_05.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 5 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_10.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_15.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 15 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_20.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_25.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 25 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

298_trofy_11_ben_30.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 298 K in .ndx format.

application/octet-stream

Label:

350_ben_10.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_ben_20.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_ben_60.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_huq_11_pnp_10.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 10 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_huq_11_pnp_20.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 20 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_huq_11_pnp_30.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 30 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_pnp_10.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 10 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_pnp_20.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 20 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_pnp_60.ndx

Text:

Index file of the simulation box of the pore without surface functionalization with 60 p-nitrophenol molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_ben_030.ndx

Text:

Index file of the simulation box of the slit-pore without surface functionalization with 30 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_ben_060.ndx

Text:

Index file of the simulation box of the slit-pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_ben_180.ndx

Text:

Index file of the simulation box of the slit-pore without surface functionalization with 180 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_trofy_11_ben_030.ndx

Text:

Index file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_trofy_11_ben_060.ndx

Text:

Index file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_slit_trofy_11_ben_180.ndx

Text:

Index file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 180 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_trofy_11_ben_10.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_trofy_11_ben_20.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

350_trofy_11_ben_30.ndx

Text:

Index file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .ndx format.

application/octet-stream

Label:

benzene.gro

Text:

Cartesian coordinates of a single benzene molecule in .gro format.

application/octet-stream

Label:

nitrophenol.gro

Text:

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

application/octet-stream

Label:

sodium.gro

Text:

Cartesian coordinates of a single sodium molecule in .gro format.

application/octet-stream

Label:

spc216.gro

Text:

Cartesian coordinates of a single water molecule in .gro format.

application/octet-stream

Label:

298_ben_10.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_ben_20.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_ben_60.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_05_ben_20.gro

Text:

Cartesian coordinates of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_05_ben_40.gro

Text:

Cartesian coordinates of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 40 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_05_ben_60.gro

Text:

Cartesian coordinates of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_05.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 5 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_10.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_15.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 15 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_20.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_25.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 25 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

298_trofy_11_ben_30.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 298 K in .gro format.

application/octet-stream

Label:

350_ben_10.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_ben_20.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_ben_60.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_huq_11_pnp_10.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 10 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_huq_11_pnp_20.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 20 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_huq_11_pnp_30.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 30 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_pnp_10.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 10 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_pnp_20.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 20 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_pnp_60.gro

Text:

Cartesian coordinates of the simulation box of the pore without surface functionalization with 60 p-nitrophenol molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_ben_030.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore without surface functionalization with 30 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_ben_060.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_ben_180.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore without surface functionalization with 180 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_trofy_11_ben_030.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_trofy_11_ben_060.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_slit_trofy_11_ben_180.gro

Text:

Cartesian coordinates of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 180 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_trofy_11_ben_10.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_trofy_11_ben_20.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

350_trofy_11_ben_30.gro

Text:

Cartesian coordinates of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .gro format.

application/octet-stream

Label:

propylamine.gro

Text:

Cartesian coordinates of a propyl-amine surface molecule in .gro format.

application/octet-stream

Label:

298_bcd_1_ben_1_unbiased.gro

Text:

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.

application/octet-stream

Label:

298_bcd_1_pnp_1_unbiased.gro

Text:

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.

application/octet-stream

Label:

350_bcd_1_ben_1_unbiased.gro

Text:

Cartesian coordinates of the unbiased free energy simulation state with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules simulated at 350 K in .gro format.

application/octet-stream

Label:

350_bcd_1_pnp_1_unbiased.gro

Text:

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 350 K in .gro format.

application/octet-stream

Label:

acd.top

Text:

Topology file of an alpha-CD molecule in .top format.

application/octet-stream

Label:

acd_huq.top

Text:

Topology file of an alpha-CD molecule with a Huq surface linker in .top format.

application/octet-stream

Label:

acd_trofy.top

Text:

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

application/octet-stream

Label:

bcd.top

Text:

Topology file of a beta-CD molecule in .top format.

application/octet-stream

Label:

bcd_huq.top

Text:

Topology file of a beta-CD molecule with a Huq surface linker in .top format.

application/octet-stream

Label:

bcd_trofy.top

Text:

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

application/octet-stream

Label:

gcd.top

Text:

Topology file of a gamma-CD molecule in .top format.

application/octet-stream

Label:

gcd_huq.top

Text:

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

application/octet-stream

Label:

gcd_trofy.top

Text:

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

application/octet-stream

Label:

bcd_1_ben_1.top

Text:

Main topology file of the free energy simulation with 1 beta-CD molecule and 1 benzene molecule in 1000 water molecules in .top format.

application/octet-stream

Label:

bcd_1_pnp_1.top

Text:

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

application/octet-stream

Label:

ben_1.top

Text:

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

application/octet-stream

Label:

pnp_1.top

Text:

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

application/octet-stream

Label:

grid.itp

Text:

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

application/vnd.shana.informed.formtemplate

Label:

benzene.top

Text:

Topology file of a benzene molecule in .top format.

application/octet-stream

Label:

nitrophenol.top

Text:

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

application/octet-stream

Label:

sodium.top

Text:

Topology file of a sodium molecule in .top format.

application/octet-stream

Label:

tip3p.top

Text:

Topology file of a water molecule in .top format.

application/octet-stream

Label:

298_ben_10.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_ben_20.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_ben_60.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_05_ben_20.top

Text:

Main topology file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_05_ben_40.top

Text:

Main topology file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 40 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_05_ben_60.top

Text:

Main topology file of the simulation box of the pore with 5 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_05.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 5 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_10.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_15.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 15 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_20.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_25.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 25 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

298_trofy_11_ben_30.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 298 K in .top format.

application/octet-stream

Label:

350_ben_10.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 10 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_ben_20.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 20 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_ben_60.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_huq_11_pnp_10.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 10 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_huq_11_pnp_20.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 20 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_huq_11_pnp_30.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Huq linker with 30 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_pnp_10.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 10 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_pnp_20.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 20 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_pnp_60.top

Text:

Main topology file of the simulation box of the pore without surface functionalization with 60 p-nitrophenol molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_ben_030.top

Text:

Main topology file of the simulation box of the slit-pore without surface functionalization with 30 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_ben_060.top

Text:

Main topology file of the simulation box of the slit-pore without surface functionalization with 60 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_ben_180.top

Text:

Main topology file of the simulation box of the slit-pore without surface functionalization with 180 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_trofy_11_ben_030.top

Text:

Main topology file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_trofy_11_ben_060.top

Text:

Main topology file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 60 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_slit_trofy_11_ben_180.top

Text:

Main topology file of the simulation box of the slit-pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 180 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_trofy_11_ben_10.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 10 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_trofy_11_ben_20.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 20 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

350_trofy_11_ben_30.top

Text:

Main topology file of the simulation box of the pore with 11 beta-CD molecules attached to the surface using a Trofymchuk linker with 30 Benzene molecules in water simulated at 350 K in .top format.

application/octet-stream

Label:

propylamine.top

Text:

Topology file of a propyl-amine surface molecule in .top format.

application/octet-stream

Label:

propylamineg.itp

Text:

Topology file of a geminal propyl-amine surface molecule in .itp format.

application/vnd.shana.informed.formtemplate

Label:

huq_350_11_1mus_7.5ns-p-s.mp4

Text:

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.

video/mp4

Label:

trofy_298_05_1mus_7.5ns-p-s.mp4

Text:

MD Simulation trajectory of 1 mus simulated at 298 K of a Pore with 5 beta-CD molecules attached to the surface using the Trofymchuk linker with 30 benzene molecules in water. Hereby one video second corresponds to 7.5 ns.

video/mp4

Label:

trofy_298_11_1mus_7.5ns-p-s.mp4

Text:

MD Simulation trajectory of 1 mus simulated at 298 K of a Pore with 11 beta-CD molecules attached to the surface using the Trofymchuk linker with 30 benzene molecules in water. Hereby one video second corresponds to 7.5 ns.

video/mp4

Label:

trofy_350_11_1mus_7.5ns-p-s.mp4

Text:

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

video/mp4