NMRDfromMD

NMRDfromMD is a Python toolkit that computes the longitudinal (\(T_1\)) and transverse (\(T_2\)) NMR relaxation times from the dipolar interaction between nuclear spins. These quantities are sensitive to molecular dynamics across a broad range of timescales, making them a powerful probe of translational and rotational motion in liquids, confined fluids, polymers, and biological systems. Used in combination with experiments, NMRDfromMD enables the validation of numerical models and helps identify the molecular mechanisms underlying relaxation. In the absence of experimental data, it can be used to interpret and predict NMR relaxation behavior from molecular dynamics simulations alone.

Compatible Simulation Packages

NMRDfromMD accepts any trajectory format supported by MDAnalysis, covering virtually all major MD simulation packages including LAMMPS, GROMACS, NAMD, AMBER, CHARMM, and many others. For a full list of supported formats, see the MDAnalysis documentation.

This package builds on the now discontinued NMRforMD.

molecular dynamics systems used in these examples molecular dynamics systems used in these examples

Figure: NMRDfromMD can be applied to a wide range of systems, from simple bulk fluids (water, left) to structureless Lennard-Jones models (center) and complex biomolecular environments such as a lysozyme protein surrounded by a hydration shell (right).

Datasets

Two molecular dynamics datasets are available on GitHub: a polymer in water system generated using LAMMPS, and a water confined in silica system generated using GROMACS. These datasets can be downloaded to follow the tutorials or simply to test NMRDfromMD.