https://github.com/simongravelle/water-in-silica
Raw data files for NMRforMD
https://github.com/simongravelle/water-in-silica
Last synced: 10 months ago
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Raw data files for NMRforMD
- Host: GitHub
- URL: https://github.com/simongravelle/water-in-silica
- Owner: simongravelle
- License: gpl-3.0
- Created: 2024-01-04T13:12:08.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-01-09T21:40:54.000Z (almost 2 years ago)
- Last Synced: 2025-01-01T13:07:56.969Z (11 months ago)
- Language: Python
- Homepage:
- Size: 87.6 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Data file for NMRforMD: water in silica slit
Raw trajectory files used for the
anisotropic tutorial of [nmrformd](https://nmrformd.readthedocs.io).
The GROMACS input files and topology are also given.
## Simulation
The system is made of 602 ($\text{TIP4P}-\epsilon$) water molecules
in a slit silica nanopore. The trajectory was recorded
during a $10 \text{ns}$ production run performed with the open source code GROMACS
in the anisotropic NPzT ensemble using a timestep of $1 \text{fs}$.
In order to balance the charge of the surface, 20 sodium ions are
present in the slit.
The imposed was temperature $T = 300^\circ\text{K}$, and the pressure
$p = 1 \text{bar}$. The positions of the atoms were recorded in
the *prod.xtc* file every $2 \text{ps}$.
## Acknowledgments
This project has received funding from the European
Union's Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement No 101065060.
