update best practice

docs/build.sh

@@ -1,2 +1,8 @@
+#!/bin/bash
+
+cd references/
+python3 filter-reference.py
+cd ..
+
 make clean
 make html

docs/references/filter-reference.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+zotero_file = open("from-zotero.bib", "r")
+cleaned_file = open("../source/references.bib", "w")
+
+for line in zotero_file:
+
+    if "journaltitle =" in line:
+        line = line.replace("journaltitle", "journal")
+
+    if ("date =" in line) & (("urldate =" not in line)):
+        if "-" in line:
+            year = line.split("-")[0].split("{")[1]
+        else:
+            year = line.split("}")[0].split("{")[1]
+        assert len(year) == 4
+        line = "  year = {"+year+"},\n"
+
+    if ("shortjournal =" not in line) & \
+        ("keywords =" not in line) & \
+        ("abstract =" not in line) & \
+        ("urldate =" not in line) & \
+        ("langid =" not in line) & \
+        ("file =" not in line):
+
+        cleaned_file.write(line)
+
+zotero_file.close()
+cleaned_file.close()

docs/references/from-zotero.bib

@@ -81,6 +81,18 @@ @article{aidasQuantumMechanicsMolecular2013
   file = {/home/simon/snap/zotero-snap/common/Zotero/storage/WIEB8525/Aidas et al. - 2013 - A quantum mechanicsmolecular dynamics study of el.pdf}
 }
 
+@book{allenComputerSimulationLiquids2017,
+  title = {Computer Simulation of Liquids},
+  author = {Allen, M. P. and Tildesley, D. J.},
+  date = {2017},
+  edition = {Second edition},
+  publisher = {{Oxford University Press}},
+  location = {{Oxford, United Kingdom}},
+  isbn = {978-0-19-880319-5 978-0-19-880320-1},
+  pagetotal = {626},
+  keywords = {Data processing,Liquids,Mathematical models,Molecular dynamics,Monte Carlo method}
+}
+
 @article{amayuelasMechanismWaterIntrusion2023,
   title = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}: {{Liquid Is Not Vapor}}},
   shorttitle = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}},
@@ -1091,6 +1103,20 @@ @article{frauxStructureDynamicsThermodynamics2019
   file = {/home/simon/snap/zotero-snap/common/Zotero/storage/SKTCJED5/Fraux et al. - 2019 - Structure, Dynamics, and Thermodynamics of Intrude.pdf}
 }
 
+@book{frenkelUnderstandingMolecularSimulation2002,
+  title = {Understanding Molecular Simulation: From Algorithms to Applications},
+  shorttitle = {Understanding Molecular Simulation},
+  author = {Frenkel, Daan and Smit, Berend},
+  date = {2002},
+  series = {Computational Science Series},
+  edition = {2nd ed},
+  number = {Volume 1},
+  publisher = {{Academic press}},
+  location = {{San Diego}},
+  isbn = {978-0-12-267351-1},
+  langid = {english}
+}
+
 @article{friesMonteCarloCalculation1983,
   title = {Monte {{Carlo}} Calculation of the Intermolecular Dipolar Spin Relaxation in a Liquid Solution},
   author = {Fries, P. H. and Belorizky, E.},

docs/source/references.bib

@@ -57,6 +57,17 @@ @article{aidasQuantumMechanicsMolecular2013
   url = {http://xlink.rsc.org/?DOI=C2CP41993A},
 }
 
+@book{allenComputerSimulationLiquids2017,
+  title = {Computer Simulation of Liquids},
+  author = {Allen, M. P. and Tildesley, D. J.},
+  year = {2017},
+  edition = {Second edition},
+  publisher = {{Oxford University Press}},
+  location = {{Oxford, United Kingdom}},
+  isbn = {978-0-19-880319-5 978-0-19-880320-1},
+  pagetotal = {626},
+}
+
 @article{amayuelasMechanismWaterIntrusion2023,
   title = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}: {{Liquid Is Not Vapor}}},
   shorttitle = {Mechanism of {{Water Intrusion}} into {{Flexible ZIF-8}}},
@@ -784,6 +795,19 @@ @article{frauxStructureDynamicsThermodynamics2019
   url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.9b02718},
 }
 
+@book{frenkelUnderstandingMolecularSimulation2002,
+  title = {Understanding Molecular Simulation: From Algorithms to Applications},
+  shorttitle = {Understanding Molecular Simulation},
+  author = {Frenkel, Daan and Smit, Berend},
+  year = {2002},
+  series = {Computational Science Series},
+  edition = {2nd ed},
+  number = {Volume 1},
+  publisher = {{Academic press}},
+  location = {{San Diego}},
+  isbn = {978-0-12-267351-1},
+}
+
 @article{friesMonteCarloCalculation1983,
   title = {Monte {{Carlo}} Calculation of the Intermolecular Dipolar Spin Relaxation in a Liquid Solution},
   author = {Fries, P. H. and Belorizky, E.},

docs/source/theory/best-practice.rst

@@ -1,8 +1,8 @@
 Best practice
 =============
 
-Choosing the force field
-------------------------
+Choosing the right force field
+------------------------------
 
 .. container:: justify
 
@@ -14,12 +14,12 @@ Choosing the force field
     it is important to keep in mind that force fields are often parametrized
     to reproduce thermodynamic quantities, such as solvation energy.
     However, NMR relaxation times depend on both structural
-    and dynamical quantities, differences between experiments
-    and simulations can be expected for the less accurate force field.
+    and dynamical quantities, and large differences between experiments
+    and simulations are expected for poorly accurate force fields.
 
 .. container:: justify
 
-    Here, as an illustration, the NMR relaxation time :math:`T_1`
+    As an illustration, the NMR relaxation time :math:`T_1`
     of bulk water was measured as a function of the temperature
     for three different water models:
     :math:`\text{TIP4P}-\epsilon` :cite:`fuentes-azcatlNonPolarizableForceField2014`,
@@ -61,10 +61,22 @@ Simulation accuracy
 
 .. container:: justify
 
-    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 (LJ) interaction has a slight impact
-    on the value of the inter-molecular :math:`T_1^\text{inter}` :cite:`gravelleNMRInvestigationWater2023`.
+    NMR relaxation measurements are sensitive both thermodynamic and dynamic quantities, 
+    and it is therefore important to ensure the accuracy of the molecular simulation.
+    Several parameters are known to affect the accuracy of the simulations,
+    such as the force field (as discussed previously), the time step, the cut-offs,
+    or the sampling time :math:`frenkelUnderstandingMolecularSimulation2002, allenComputerSimulationLiquids2017`.
+
+.. container:: justify
+
+    As an illustration, the NMR relaxation time :math:`T_1`
+    of bulk water was measured as a function of the LJ cut-off.
+    Our results show that, for the smallest cut-off,
+    the inter-molecular :math:`T_1^\text{inter}` is slightly
+    under-estimated, which is mainly due to an over-estimation
+    of the inter-molecular characteristic time :math:`\tau_\text{inter}`.
+    These observations are consistent
+    with previous measurements :cite:`gravelleNMRInvestigationWater2023`.
 
 .. image:: ../figures/illustrations/bulk-water/effect_cutoff-dark.png
     :class: only-dark

docs/source/theory/context.rst

@@ -21,7 +21,8 @@ Context
     water and other small molecules :cite:`lippensT1RelaxationTime1993, calero1HNuclearSpin2015, singerMolecularDynamicsSimulations2017, singerNMRSpinrotationRelaxation2018, philipsProtonNMRRelaxation2019, singerElucidatingNMRRelaxation2020`.
     MDS are also used to study the NMR relaxation properties of molecules confined within
     nanoporous materials :cite:`khudozhitkovDynamicsPropenePropane2020, gravelleNMRInvestigationWater2023`,
-    as well as large polymer molecules, lipid membranes, and proteins.
+    as well as large polymer molecules, lipid membranes, proteins,
+    or glass transition phenomenon of glycerol :cite:`becherMolecularDynamicsSimulations2021`.
 
 .. container:: justify
 
@@ -31,13 +32,7 @@ Context
     :cite:`philipsQuadrupolarNMRRelaxation2020, chubakNMRRelaxationRates2021`,
     which is beyond the scope of the present contribution.
     Monte carlo simulations have also been used :cite:`friesMonteCarloCalculation1983`,
-    although in that case some care must be taken to extract time dependant quantities
+    although, in that case, some care must be taken to extract time-dependant quantities
     such as autocorrelation functions :cite:`huitemaCanMonteCarlo1999`. Recently,
-    the possibility to calculate NMR relaxation rate from coarse grained models was also
-    discussed :cite:`gravelleAssessingValidityNMR2023`. 
-
-.. container:: justify
-
-    Authors have also directly combined simulations and experiments, for instance to study
-    glass transition phenomenon of glycerol :cite:`becherMolecularDynamicsSimulations2021`,
-    water confined within salt crusts :cite:`gravelleNMRInvestigationWater2023`
+    the possibility to calculate NMR relaxation rate from coarse grained models
+    whose atomic details were reconstructed a posteriori was demonstrated :cite:`gravelleAssessingValidityNMR2023`.