nmrformd 0.0.8

Calculate NMR relaxation time from molecular dynamics trajectory file

NMRforMD is a python script 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, GROMACS, or AMBER simulation package.

Information

NMRforMD is in development and likely to return errors. Please raise an issue here if you find one.

For details and a tutorial, have a look at the documentation.

Installation

Using pip, type in a terminal:

pip install nmrformd

Or, clone this repository on your computer and use pip from the main directory:

git clone [e-mail]:simongravelle/nmrformd.git

cd nmrformd/

pip install .

You can run the test using pytest:

cd tests
pytest mytest.py

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", "full", 0, "m0")

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

• currently only residues have been tested

• the code has mostly been tested with GROMACS trajectory file