Metadata-Version: 2.1
Name: nmrformd
Version: 0.1.0
Summary: Calculate NMR relaxation time from                    molecular dynamics trajectory file
Home-page: https://github.com/simongravelle/nmrformd
Author: Simon Gravelle
Author-email: simon.gravelle@live.fr
License: GNU GENERAL PUBLIC LICENSE
Download-URL: https://github.com/simongravelle/nmrformd/releases/download/v0.1.0/nmrformd-0.1.0.tar.gz
Platform: UNKNOWN
Description-Content-Type: text/x-rst
Requires-Dist: mdanalysis
Requires-Dist: numpy
Requires-Dist: pytest
Requires-Dist: scipy

.. image:: https://readthedocs.org/projects/nmrformd/badge/?version=latest

.. image:: https://raw.githubusercontent.com/simongravelle/nmrformd/main/docs/source/images/NMRforMD_READMEc.png

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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.

..
	This documentation is separated in four parts: tutorials, how-to scripts,
	description, and theory.

.. _`MDAnalysis`: https://www.mdanalysis.org/
.. _`LAMMPS`: https://www.lammps.org/
.. _`GROMACS`: https://www.gromacs.org/
.. _`Github`: https://github.com/simongravelle/nmrformd

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


.. image:: https://raw.githubusercontent.com/simongravelle/nmrformd/main/docs/source/images/main_image.png

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. 

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

Installation
------------

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Using pip, type in a terminal:

.. code-block:: bash

	pip3 install nmrformd

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

.. code-block:: bash

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

	cd nmrformd/

	pip install .

You can run the tests using pytest:

.. code-block:: bash	

	cd tests
	pytest .

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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.

.. _`tutorial`: https://nmrformd.readthedocs.io/en/latest/documentation_pages/tutorial1.html

.. code-block:: python3

	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``.

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Known issues
------------

- for very large trajectory file, the code requires a lot of memory
- the code has only beed tested with hydrogen atoms

.. _`documentation`: https://nmrformd.readthedocs.io/en/latest/



