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simongravelle committed Dec 29, 2023
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18 changes: 9 additions & 9 deletions docs/source/tutorials/isotropic-system.rst
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Expand Up @@ -29,9 +29,6 @@ Isotropic systems

<a href="https://www.matplotlib.org" target="_blank">matplotlib</a>

System
------

.. image:: ../figures/tutorials/polymer-in-water/peg-dark.png
:class: only-dark
:alt: PEG-water mixture simulated with GROMACS - Dipolar NMR relaxation time calculation
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:width: 250
:align: right

MD system
---------

.. container:: justify

The system is made of a bulk mixture of 320 :math:`\text{TIP4P}-\epsilon` water molecules
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<a href="https://lammpstutorials.github.io/" target="_blank">tutorials</a>

File preparation and libraries
------------------------------
File preparation
----------------

.. container:: justify

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as submodule. The dataset needed to follow this tutorial is located
in *nmrformd-data/polymer-in-water/raw-data/NPEG32/*.

Create a MDAnalysis universe
----------------------------

.. container:: justify

Open a new Python script or a new notebook, and define
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.. container:: justify

Also import numpy, MDAnalysis, and NMRforMD:
Then, import numpy, MDAnalysis, and NMRforMD:

.. code-block:: python
import numpy as np
import MDAnalysis as mda
import nmrformd as nmrmd
Create a MDAnalysis universe
----------------------------

.. container:: justify

From the trajectory files, let us create a MDAnalysis universe.
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