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simongravelle committed Dec 29, 2023
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28 changes: 22 additions & 6 deletions docs/source/tutorials/isotropic-system.rst
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In this tutorial, the NMR relaxation times :math:`T_1` and :math:`T_2`
are measured from a bulk polymer-water mixture using
*NMRforMD*. `MDAnalysis <https://www.mdanalysis.org>`__,
`numpy <https://www.numpy.org>`__, and
`matplotlib <https://www.matplotlib.org>`__ and *NMRforMD* must be
are measured from a bulk polymer-water mixture using |NMRforMD| .
|MDAnalysis|,
|numpy|, and
|matplotlib| and *NMRforMD* must be
installed.

.. |NMRforMD| raw:: html

<a href="https://nmrformd.readthedocs.io" target="_blank">NMRforMD</a>

.. |MDAnalysis| raw:: html

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

.. |numpy| raw:: html

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

.. |matplotlib| raw:: html

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

System
------

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and 32 :math:`\text{PEG}300` polymer molecules. The trajectory was recorded
during a :math:`10\,\text{ns}` production run performed with the open source code LAMMPS
in the NPT ensemble using a timestep of :math:`1\,\text{fs}`.
The imposed was temperature :math:`T = 300^\circ\text{K}`, and the pressure
:math:`p = 1^\circ\text{atm}`. The positions of the atoms were recorded in
The imposed was temperature :math:`T = 300\,^\circ\text{K}`, and the pressure
:math:`p = 1\,\text{atm}`. The positions of the atoms were recorded in
a a file every :math:`1\,\text{ps}`.

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