Protein-in-water Dataset for NMRDfromMD

GROMACS input files and raw trajectory files used to generate the data and figure from nmrdfrommd. The system consists of a protein (HEWL) in water.

Repository structure

• inputs: Contains the LAMMPS input files.
• data: Contains simulation output files (.data and .lammpstrj) for various temperatures, generated from the input files. Due to their large size, .xtc files are not hosted in this repository. You can regenerate them by relaunching the simulation with LAMMPS.
• 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

This repository uses Git LFS (Large File Storage) to store large trajectory files. First, install Git LFS if it is not already available:

sudo apt install git-lfs

Initialize Git LFS

git lfs install

Then clone the repository:

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

Download all Git LFS files:

git lfs pull

Regenerate the trajectory

To regenerate the trajectory files, navigate to the data folder. Then, update the path to GROMACS in run-all.sh to reflect your system configuration, then, execute run-all.sh.

License

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