View: |
Part 1: Document Description
|
Citation |
|
---|---|
Title: |
Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' |
Identification Number: |
doi:10.18419/darus-2154 |
Distributor: |
DaRUS |
Date of Distribution: |
2022-03-09 |
Version: |
1 |
Bibliographic Citation: |
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 |
Citation |
|
Title: |
Supplementary material for 'An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica' |
Identification Number: |
doi:10.18419/darus-2154 |
Authoring Entity: |
Kraus, Hamzeh (University of Stuttgart) |
Hansen, Niels (University of Stuttgart) |
|
Grant Number: |
358283783 - SFB 1333 |
Distributor: |
DaRUS |
Access Authority: |
Kraus, Hamzeh |
Access Authority: |
Hansen, Niels |
Depositor: |
Kraus, Hamzeh |
Date of Deposit: |
2021-09-21 |
Holdings Information: |
https://doi.org/10.18419/darus-2154 |
Study Scope |
|
Keywords: |
Chemistry, Computer and Information Science, Molecular Dynamics Simulation, Adsorption, Cyclodextrins, Mesoporous Silica |
Abstract: |
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. |
Methodology and Processing |
|
Sources Statement |
|
Data Access |
|
Other Study Description Materials |
|
Related Publications |
|
Citation |
|
Title: |
Kraus, H. & Hansen, N. (2022): An atomistic view on the uptake of aromatic compounds by cyclodextrin immobilized on mesoporous silica. Adsorption. |
Identification Number: |
10.1007/s10450-022-00356-w |
Bibliographic Citation: |
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. |
Notes: |
text/x-sh |
Label: |
poreana.ipynb |
Text: |
Jupyter-Notebook for pore trajectory analysis using the PoreAna python package. |
Notes: |
application/x-ipynb+json |
Label: |
porems.ipynb |
Text: |
Jupyter-Notebook for pore system generation using the PoreMS python package. |
Notes: |
application/x-ipynb+json |
Label: |
poresim.ipynb |
Text: |
Jupyter-Notebook for pore simulation preparation for GROMACS using the PoreSim python package. |
Notes: |
application/x-ipynb+json |
Label: |
pore_clear.pms |
Text: |
PoreMS object file of the pore without functionalization in pickle format protocol version 3. |
Notes: |
application/x-tgif |
Label: |
pore_system_clear.pms |
Text: |
PoreMS object file of the pore system without functionalization in pickle format protocol version 3. |
Notes: |
application/x-tgif |
Label: |
pore_clear_slit.pms |
Text: |
PoreMS object file of the slit-pore without functionalization in pickle format protocol version 3. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
run_biased.mdp |
Text: |
Simulation parameter file of the production step of the biased free energy simulation in .mdp format. |
Notes: |
application/octet-stream |
Label: |
min_pore.mdp |
Text: |
Simulation parameter file of the energy-minimization step of the pore simulation in .mdp format. |
Notes: |
application/octet-stream |
Label: |
nvt_pore.mdp |
Text: |
Simulation parameter file of the NVT equilibration step of the pore simulation in .mdp format. |
Notes: |
application/octet-stream |
Label: |
run_pore.mdp |
Text: |
Simulation parameter file of the production step of the pore simulation in .mdp format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
acd.gro |
Text: |
Cartesian coordinates of an alpha-CD molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
acd_huq.gro |
Notes: |
application/octet-stream |
Label: |
acd_trofy.gro |
Text: |
Cartesian coordinates of an alpha-CD molecule with a Trofymchuk surface linker in .gro format. |
Notes: |
application/octet-stream |
Label: |
bcd.gro |
Text: |
Cartesian coordinates of a beta-CD molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
bcd_huq.gro |
Text: |
Cartesian coordinates of a beta-CD molecule with a Huq surface linker in .gro format. |
Notes: |
application/octet-stream |
Label: |
bcd_trofy.gro |
Text: |
Cartesian coordinates of a beta-CD molecule with a Trofymchuk surface linker in .gro format. |
Notes: |
application/octet-stream |
Label: |
gcd.gro |
Text: |
Cartesian coordinates of a gamma-CD molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
gcd_huq.gro |
Text: |
Cartesian coordinates of a gamma-CD molecule with a Huq surface linker in .gro format. |
Notes: |
application/octet-stream |
Label: |
gcd_trofy.gro |
Text: |
Cartesian coordinates of a gamma-CD molecule with a Trofymchuk surface linker in .gro format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
benzene.gro |
Text: |
Cartesian coordinates of a single benzene molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
nitrophenol.gro |
Text: |
Cartesian coordinates of a single p-nitrophenol molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
sodium.gro |
Text: |
Cartesian coordinates of a single sodium molecule in .gro format. |
Notes: |
application/octet-stream |
Label: |
spc216.gro |
Text: |
Cartesian coordinates of a single water molecule in .gro format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
propylamine.gro |
Text: |
Cartesian coordinates of a propyl-amine surface molecule in .gro format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
acd.top |
Text: |
Topology file of an alpha-CD molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
acd_huq.top |
Text: |
Topology file of an alpha-CD molecule with a Huq surface linker in .top format. |
Notes: |
application/octet-stream |
Label: |
acd_trofy.top |
Text: |
Topology file of an alpha-CD molecule with a Trofymchuk surface linker in .top format. |
Notes: |
application/octet-stream |
Label: |
bcd.top |
Text: |
Topology file of a beta-CD molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
bcd_huq.top |
Text: |
Topology file of a beta-CD molecule with a Huq surface linker in .top format. |
Notes: |
application/octet-stream |
Label: |
bcd_trofy.top |
Text: |
Topology file of a beta-CD molecule with a Trofymchuk surface linker in .top format. |
Notes: |
application/octet-stream |
Label: |
gcd.top |
Text: |
Topology file of a gamma-CD molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
gcd_huq.top |
Text: |
Topology file of a gamma-CD molecule with a Huq surface linker in .top format. |
Notes: |
application/octet-stream |
Label: |
gcd_trofy.top |
Text: |
Topology file of a gamma-CD molecule with a Trofymchuk surface linker in .top format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
grid.itp |
Text: |
Topology file of all used grid molecules of the pore system in .itp format. |
Notes: |
application/vnd.shana.informed.formtemplate |
Label: |
benzene.top |
Text: |
Topology file of a benzene molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
nitrophenol.top |
Text: |
Topology file of a p-nitrophenol molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
sodium.top |
Text: |
Topology file of a sodium molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
tip3p.top |
Text: |
Topology file of a water molecule in .top format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
application/octet-stream |
Label: |
propylamine.top |
Text: |
Topology file of a propyl-amine surface molecule in .top format. |
Notes: |
application/octet-stream |
Label: |
propylamineg.itp |
Text: |
Topology file of a geminal propyl-amine surface molecule in .itp format. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
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. |
Notes: |
video/mp4 |