Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining" (doi:10.18419/darus-4494)

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Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"

doi:10.18419/darus-4494

DaRUS

2024-10-16

1

Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2024, "Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"", https://doi.org/10.18419/darus-4494, DaRUS, V1

Scripts and data for "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining"

doi:10.18419/darus-4494

Gravelle, Simon (Université Grenoble Alpes - UGA)

Beyer, David (Universität Stuttgart)

Brito, Mariano E. (Universität Stuttgart)

Schlaich, Alexander (Universität Stuttgart)

Holm, Christian (Universität Stuttgart)

Python

GROMACS

327154368 - SFB 1313

EXC 2075 - 390740016

info:eu-repo/grantAgreement/EC/HE/101065060

DaRUS

Gravelle, Simon

Huber, Frank

Gravelle, Simon

2024-09-22

https://doi.org/10.18419/darus-4494

Chemistry, Physics, Molecular Dynamics Simulation, GROMACS, NMR Spectroscopy, Python

Simulations and data analysis scripts for the publication "Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining". Within gromacs-inputs, two types of GROMACS simulation scripts are provided: all-atom and united-atoms. In both cases, the system is a liquid propane bulk system. See the <a href="https://darus.uni-stuttgart.de/file.xhtml?fileId=320568">README</a> file for details and instructions. In addition, Python scripts for reconstructing united-atom trajectories into all-atom are provided within trajectory-conversion.

Simon Gravelle, David Beyer, Mariano Brito, Alexander Schlaich, Christian Holm: Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining

Simon Gravelle, David Beyer, Mariano Brito, Alexander Schlaich, Christian Holm: Calculation of 1H-NMR relaxation rates from a model united-atom alkanes using reverse coarse-graining

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README.md

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Readme file

text/markdown

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conf.gro

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GROMACS topology file

application/octet-stream

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topol.top

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GROMACS force field

application/octet-stream

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C3H8.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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ffbonded.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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ffnonbonded.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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ff_dum.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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forcefield.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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min.mdp

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GROMACS input

application/octet-stream

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npt.mdp

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GROMACS input

application/octet-stream

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nvt.mdp

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GROMACS input

application/octet-stream

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prod.mdp

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GROMACS input

application/octet-stream

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conf.gro

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GROMACS topology

application/octet-stream

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topol.top

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GROMACS topology

application/octet-stream

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ffbonded.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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ffnonbonded.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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ff_dum.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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forcefield.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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propane.itp

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GROMACS force field

application/vnd.shana.informed.formtemplate

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min.mdp

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GROMACS input

application/octet-stream

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npt.mdp

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GROMACS input

application/octet-stream

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nvt.mdp

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GROMACS input

application/octet-stream

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prod.mdp

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GROMACS input

application/octet-stream

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README.md

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Readme file

text/markdown

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convert-AA-to-AAr.ipynb

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Notebook for converting the sample trajectory

application/x-ipynb+json

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AA-molecule.xtc

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Trajectory sample

application/octet-stream

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AA-single-molecule.gro

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Trajectory sample

application/octet-stream

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AA.gro

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Trajectory sample

application/octet-stream

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AA.tpr

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Trajectory sample

application/octet-stream

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AA.xtc

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Trajectory sample

application/octet-stream

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topol.top

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Trajectory sample

application/octet-stream

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converters.py

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Python script for converting trajectories

text/x-python

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hydrogen_from_carbon.py

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Python script for converting trajectories

text/x-python

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make_AAr.py

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Python script for converting trajectories

text/x-python

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make_carbon_from_AA.py

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Python script for converting trajectories

text/x-python

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make_carbon_from_com.py

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Python script for converting trajectories

text/x-python

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make_united_atom.py

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Python script for converting trajectories

text/x-python

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propane_structure.py

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Python script for converting trajectories

text/x-python

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utilities.py

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Python script for converting trajectories

text/x-python

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convert-UA-to-UAr.ipynb

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Notebook for converting the sample trajectory

application/x-ipynb+json

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topol.top

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Trajectory sample

application/octet-stream

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UA-molecule.xtc

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Trajectory sample

application/octet-stream

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UA.gro

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Trajectory sample

application/octet-stream

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UA.tpr

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Trajectory sample

application/octet-stream

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UA.xtc

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Trajectory sample

application/octet-stream