changed data structure

.gitmodules

@@ -1,6 +1,21 @@
-[submodule "nmrformd-data"]
-	path = nmrformd-data
-	url = [email protected]:simongravelle/nmrformd-data.git
 [submodule "examples/pyplot-perso"]
 	path = examples/pyplot-perso
 	url = [email protected]:simongravelle/pyplot-perso.git
+[submodule "data/bulk-water-tip4p"]
+	path = data/bulk-water-tip4p
+	url = [email protected]:simongravelle/bulk-water-tip4p.git
+[submodule "data/water-in-silica"]
+	path = data/water-in-silica
+	url = [email protected]:simongravelle/water-in-silica.git
+[submodule "data/bulk-water-high-dumping-rate"]
+	path = data/bulk-water-high-dumping-rate
+	url = [email protected]:simongravelle/bulk-water-high-dumping-rate.git
+[submodule "data/lennard-jones-fluid"]
+	path = data/lennard-jones-fluid
+	url = [email protected]:simongravelle/lennard-jones-fluid.git
+[submodule "data/polymer-in-water"]
+	path = data/polymer-in-water
+	url = [email protected]:simongravelle/polymer-in-water.git
+[submodule "data/HEWL-in-water"]
+	path = data/HEWL-in-water
+	url = [email protected]:simongravelle/HEWL-in-water.git

docs/source/theory/best-practice.rst

@@ -1,22 +1,30 @@
 Best practice
 =============
 
-Force field
------------
+Choosing the force field
+------------------------
 
 .. container:: justify
 
-    Force fields are usually parametrized based on thermodynamic quantities only.
-    However, NMR relaxation quantities depend on both structural and dynamical quantities. 
-
-Simulation precision
---------------------
+    The agreement between experiments and simulations can only be as good as the
+    force field used in the simulations. Although it has been shown that some
+    force fields lead to excellent agreement with experimental data, as for instance
+    for water, hydrocarbons, or polymer melts
+    :cite:`singerMolecularDynamicsSimulations2017,gravelleNMRInvestigationWater2023,gravelleAssessingValidityNMR2023`,
+    it is important to keep in mind that force fields are usually parametrized
+    based on thermodynamic quantities. Since NMR relaxation quantities
+    depend on both structural and dynamical quantities, differences between experiments
+    and simulations can sometimes be expected.
+
+Simulation accuracy
+-------------------
 
 .. container:: justify
 
-    NMR relaxation rate measurements are extremely sensitive to the precision of the
-    simulation. The cut-off, for instance, was noted to have a slight impact
-    on :math:`R_1`.
+    Since NMR relaxation rate measurements are sensitive both thermodynamic and dynamic quantities, 
+    it is important to ensure the accuracy of the simulation.
+    For instance, the cut-off for the Lennard-Jones interaction has a slight impact
+    on the value :math:`R_1` :cite:`gravelleNMRInvestigationWater2023`.
 
 Box size
 --------

examples/illustrations/bulk-water/analysis.ipynb

@@ -2,18 +2,9 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/simon/.local/lib/python3.11/site-packages/MDAnalysis/topology/TPRParser.py:161: DeprecationWarning: 'xdrlib' is deprecated and slated for removal in Python 3.13\n",
-      "  import xdrlib\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import numpy as np\n",
     "import MDAnalysis as mda\n",
@@ -22,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -34,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -104,61 +95,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "50 1 1216\n",
-      "78 1 1216\n",
-      "124 1 1216\n",
-      "198 1 1216\n",
-      "316 1 1208\n",
-      "502 1 1207\n",
-      "796 1 1207\n",
-      "1262 1 1207\n",
-      "2004 1 1201\n",
-      "3178 1 1183\n",
-      "5042 1 1180\n",
-      "8000 1 263 1.0\n",
-      "8000 1 264 1.0\n",
-      "8000 1 132 0.2\n",
-      "N: 33\n",
-      "N: 34\n",
-      "50 1 1225\n",
-      "78 1 1225\n",
-      "124 1 1225\n",
-      "198 1 1225\n",
-      "316 1 1217\n",
-      "502 1 1216\n",
-      "796 1 1216\n",
-      "1262 1 1216\n",
-      "2004 1 1210\n",
-      "3178 1 1192\n",
-      "5042 1 1189\n",
-      "8000 1 265 1.0\n",
-      "8000 1 266 1.0\n",
-      "8000 1 133 0.2\n",
-      "N: 35\n",
-      "N: 36\n",
-      "50 1 1234\n",
-      "78 1 1234\n",
-      "124 1 1234\n",
-      "198 1 1234\n",
-      "316 1 1226\n",
-      "502 1 1225\n",
-      "796 1 1225\n",
-      "1262 1 1225\n",
-      "2004 1 1219\n",
-      "3178 1 1201\n",
-      "5042 1 1198\n",
-      "8000 1 267 1.0\n",
-      "8000 1 268 1.0\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "while 1<2:\n",
     "    # varying number\n",