NMRforMD

<a href="webp"> <img src="docs/source/figures/logo/logo-b.png" align="right" width="30%"/> </a>

Dipolar Nuclear Magnetic Resonance for Molecular Dynamics (NMRforMD) simulations is a Python toolkit designed for the computation of dipolar NMR relaxation times (the so called $T_1$ and $T_2$) from molecular dynamics simulations. Used in combination with MDAnalysis, NMRforMD allows for the analysis of trajectory files from any MDAnalysis-compatible simulation package, including LAMMPS and GROMACS.

Migration

This repository will progressively be migrated on here, and the most up-to-date page will be https://nmrdfrommd.github.io.

Documentation

Details about installation and use of NMRforMD are given in the documentation. The documentation also contains a description of the theory behind dipolar dipolar NMR calculations, as well as details on some common pitfalls of NMR calculations.

<p float="left"> <a href="https://nmrformd.readthedocs.io/en/latest/"> <img src="avatars/bulk-water.png" width="32%" /> </a> <a href="https://nmrformd.readthedocs.io/en/latest/"> <img src="avatars/lennard-jones-fluid.png" width="32%" /> </a> <a href="https://nmrformd.readthedocs.io/en/latest/"> <img src="avatars/lysozyme-in-water.png" width="32%" /> </a> </p>

Figure: Examples of systems that can be analyzed using NMRforMD, from left to right: a bulk water system, a lennard-jones fluid, and a lysozyme in water.

Datasets

Two molecular dynamics datasets are available on Github. One is a polymer in water system generated using LAMMPS, the second is a water confined in silica generated using GROMACS. Both datasets are required to follow the tutorials provided in the documentation.

Warning

The code has mostly been tested in the case of 1H-NMR (i.e. spin 1/2). It is also important to keep in mind that NMRforMD only works for dipolar interaction, not quadrupolar interaction.

Known issues

For very large trajectory file, the code requires a lot of memory. The code is not adapted to triclinic box, convert your trajectory to orthorhombic prior to calculation. This code is still in development, please raise an issue here if you encounter another problem.

For developers

If you intend to make modification to the code, please raise an issue or send me an email first. Then, fork the repository, apply your changes, then make a pull request that will be reviewed.

Clone the repository with its submodules as follow:

git clone https://github.com/simongravelle/nmrformd.git --recurse-submodule

Find more instructions here.

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.