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improved tutorial
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simongravelle committed Dec 29, 2023
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.. container:: hatnote

NMR relaxation time :math:`T_1` measured from a water-polymer mixture
Measuring the NMR relaxation time from a bulk water-polymer mixture

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In this tutorial, the NMR relaxation time :math:`T_1` of water is measured using
*DNMRfromMD*. `MDAnalysis <https://www.mdanalysis.org>`__,
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
`matplotlib <https://www.matplotlib.org>`__ and *NMRforMD* must be
installed.

System
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The system is made of 334 TIP4P-:math:`\epsilon` water molecules
and 20 PEG300 polymer molecules
simulated in the NVT ensemble using GROMACS at a temperature of 295.15°K. The total
duration of the simulation is 5\,ns, and the timestep is 1 fs. You can
The system is made of 334 :math:`\text{TIP4P}-\epsilon` water molecules
and 20 `\text{PEG}-300` polymer molecules simulated in the NVT ensemble
using GROMACS at a temperature :math:`T = 295.15^\circ\text{K}`. The total
duration of the simulation is :math:`:5\,\text{ns}`, and the
timestep is :math:`1\,\text{fs}`. You can
access the input files in this |repository-examples|.

If you are not familiar with GROMACS, you can find `tutorials
here <https://gromacstutorials.github.io/>`__.


.. |repository-examples| raw:: html

<a href="https://github.com/simongravelle/nmrformd/tree/main/examples" target="_blank">repository</a>


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If you are not familiar with GROMACS, you can find `tutorials
here <https://gromacstutorials.github.io/>`__.

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