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

To clone the repository, run:

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

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

cd dataset-protein-in-water/data

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

gmx=

Then, execute run-all.sh.

License

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