nmrformd 0.1.0

Calculate NMR relaxation time from molecular dynamics trajectory file

NMRforMD is a python toolkit to calculate NMR relaxation times from molecular dynamics trajectory files. Used in combination with MDAnalysis, it allows for the analysis of trajectory files from LAMMPS and GROMACS simulation package.

Notes :

• NMRforMD is still in development, please raise an issue on Github if you encounter a problem

• the code has mostly been tested with GROMACS and LAMMPS trajectory files, but should work with other molecular dynamics packages, as long as they are compatible with MDAnalysis

• NMRforMD does not work with triclinic box, use MDAnalysis to convert your trajectory to orthorhombic

Example of systems that can be analysed using NMRforMD, from left to right: a bulk water reservoir, a PEG molecule, and water in a slit silica pore.

For details and instructions for beginners, have a look at the documentation.

Installation

Using pip, type in a terminal:

pip3 install nmrformd

To get the last version, clone this repository on your computer and use pip3 from the main directory:

git clone https://github.com/simongravelle/nmrformd.git

cd nmrformd/

pip install .

You can run the tests using pytest:

cd tests
pytest .

Basic example

This is an example showing how to use NMRforMD to measure NMR signal from a molecular dynamics simulations. See the tutorial for more information.

import MDAnalysis as mda
import nmrformd
u = mda.Universe("topology.tpr", "trajectory.xtc")
nmr_result = nmrformd.NMR(u, "type H", "type H")

The NMR relaxation time T1 is given by nmr_result.T1.

Known issues

• for very large trajectory file, the code requires a lot of memory

• the code has only beed tested with hydrogen atoms