Dipolar Nuclear Magnetic Resonance from Molecular Dynamics (NMRDfromMD) is a
Python toolkit designed for the computation of dipolar NMR relaxation times
(the so-called
Used in combination with MDAnalysis, NMRDfromMD allows for the analysis of trajectory files from any MDAnalysis-compatible simulation package, including LAMMPS and GROMACS.
Details about installation and use of NMRDfromMD are given in the documentation. The documentation also includes a description of the theory behind dipolar NMR calculations, as well as details on some common pitfalls of NMR analysis.
Figure: Examples of systems that can be analyzed using NMRDfromMD, from left to right: a bulk water system, a Lennard-Jones fluid, and a lysozyme in water.
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 system generated using GROMACS. Both datasets are required to follow the tutorials provided in the documentation.
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 NMRDfromMD only works for dipolar
interactions, not quadrupolar interactions.
For very large trajectory files, the code requires a lot of memory.
The code is not adapted to triclinic boxes — convert your trajectory to
orthorhombic before running calculations. This code is still in development,
so please raise an issue here
if you encounter a problem.
If you intend to make modifications to the code, please raise an issue or send me an email first. Then, fork the repository, apply your changes, and make a pull request that will be reviewed. Find more instructions here.
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.