Water in Silica Dataset for NMRDfromMD

GROMACS input files and raw trajectory files used to generate the data and figure from nmrdfrommd. The system consists of water confined in a slit silica pore.

Repository structure

• inputs: Contains the GROMACS input files. The readlammps pip package is required to create different systems.
• data: Contains simulation output files.
• analysis: Contains Python scripts for running NMRDfromMD and extract NMR relaxation rates.
• snapshot: Contains .png images of the system generated using VMD.

Clone the repository

To clone the repository, run:

git clone https://github.com/NMRDfromMD/dataset-water-in-silica.git

To regenerate the trajectory files, navigate to the data folder:

cd dataset-water-in-silica/data

Update the path to LAMMPS in run-all.sh to reflect your system configuration:

lmp=/home/simon/Softwares/lammps-27Jun2024/src/lmp_mpi

Then, execute run-all.sh.

License

This repository is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) License.