deploy: 519dee7

Author: simongravelle

lammpstutorials-inputs/level2/polymer-in-water/pullonPEG/gyration-radius.dat

@@ -59,6 +59,8 @@ variable z1 equal xcm(topull1,z)
 variable z2 equal xcm(topull2,z)
 variable delta_r equal sqrt((v_x1-v_x2)^2+(v_y1-v_y2)^2+(v_z1-v_z2)^2)
 fix myat2 all ave/time 10 10 100 v_delta_r file end-to-end-distance.dat
+compute rgyr PEG gyration
+fix myat3 all ave/time 10 10 100 c_rgyr file gyration-radius.dat
 thermo 1000
 
 compute bond_H2O H2O bond/local dist # engpot

lammpstutorials-inputs/level2/polymer-in-water/pullonPEG/input.lammps

@@ -186,8 +186,8 @@ System generation
 
 ..  container:: justify
 
-    Within the last three lines, a *region* named *rliquid* for depositing the
-    water molecules are created based on the last defined lattice, which is *fcc 4.04*. 
+    Within the last three lines, a *region* named *rliquid* is created based on the last defined lattice, *fcc 4.04*.
+    *rliquid* will be used for depositing the water molecules.
 
 ..  container:: justify
 
@@ -196,9 +196,9 @@ System generation
 
 ..  container:: justify
 
-    Molecules are created on the *fcc 4.04* lattice
+    The new molecules are placed on the *fcc 4.04* lattice
     by the *create_atoms* command. The
-    first parameter is '0', meaning that the atom IDs from the
+    first parameter is 0, meaning that the atom IDs from the
     *RigidH2O.txt* file will be used.
     The number *482793* is a seed that is
     required by LAMMPS, it can be any positive integer.
@@ -246,8 +246,8 @@ System generation
 
 ..  container:: justify
 
-    Create a new text file, call it *PARM.lammps*, and copy it
-    next to the *systemcreation/* folder. Copy the following lines
+    Create a new text file called *PARM.lammps* next to
+    the *systemcreation/* folder. Copy the following lines
     into PARM.lammps:
 
 ..  code-block:: lammps
@@ -265,10 +265,6 @@ System generation
     pair_coeff 5 5 11.697 2.574 # wall
     pair_coeff 1 5 0.4 2.86645 # water-wall
 
-    bond_coeff 1 0 0.9572 # water
-
-    angle_coeff 1 0 104.52 # water
-
 ..  container:: justify
 
     Each *mass* command assigns a mass in grams/mole to an atom type. Each
@@ -287,39 +283,36 @@ System generation
 
 ..  container:: justify
 
-    As already seen in previous tutorials, 
-    and with the important exception of *pair_coeff 1 5*,
-    only pairwise interaction between atoms of
-    identical types was assigned. By default, LAMMPS calculates
-    the pair coefficients for the interactions between atoms
-    of different types (i and j) by using geometrical
-    average: :math:`\epsilon_{ij} = (\epsilon_{ii} + \epsilon_{jj})/2`, 
-    :math:`\sigma_{ij} = (\sigma_{ii} + \sigma_{jj})/2.`
-    Other rules for cross coefficients can be set with the
-    *pair_modify* command, but for the sake of simplicity,
-    the default option is kept here.
+    As already seen in previous tutorials and with the important exception of 
+    *pair_coeff 1 5*, only pairwise interactions between atoms of identical
+    types was assigned. By default, LAMMPS calculates the pair coefficients for
+    the interactions between atoms of different types (i and j) by using geometrical average: 
+    :math:`\epsilon_{ij} = (\epsilon_{ii} + \epsilon_{jj})/2`, 
+    :math:`\sigma_{ij} = (\sigma_{ii} + \sigma_{jj})/2.`.
+    If the default value of :math:`5.941\,\text{kcal/mol}`
+    was kept for :math:`\epsilon_\text{1-5}`, the solid walls would be extremely
+    hydrophilic, causing the water molecule to form dense layers. As a comparison,
+    the water-water energy :math:`\epsilon_\text{1-1}` is only
+    :math:`0.185199\,\text{kcal/mol}`. Therefore, the walls were made less
+    hydrophilic by reducing the value of :math:`\epsilon_\text{1-5}`. Copy the
+    following lines into PARM.lammps as well:
 
-.. container:: justify
+..  code-block:: lammps
+
+    bond_coeff 1 0 0.9572 # water
 
-    By default, the value
-    of :math:`\epsilon_\text{1-5} = 5.941\,\text{kcal/mol}` would
-    be extremely high (compared to the water-water
-    energy :math:`\epsilon_\text{1-1} = 0.185199\,\text{kcal/mol}`),
-    which would make the surface extremely hydrophilic.
-    The walls were made less hydrophilic by reducing the 
-    LJ energy of interaction :math:`\epsilon_\text{1-5}`.
+    angle_coeff 1 0 104.52 # water
 
 ..  container:: justify
 
-    The *bond_coeff*, which is here used for the O-H bond of the water
-    molecule, sets both the energy of the harmonic
-    potential and the equilibrium distance in Ångstrom. The
-    value is *0* for the energy because we are going to use a
-    rigid model for the water molecule. The shape of the
-    molecule will be preserved later by the *shake* algorithm.
-    Similarly, the angle coefficient here for the H-O-H angle
-    of the water molecule sets the energy of the harmonic
-    potential (also 0) and the equilibrium angle is in degree.
+    The *bond_coeff* command, used here for the O-H bond of the water molecule, sets both
+    the spring constant of the harmonic potential and the equilibrium distance
+    of :math:`0.9572~\text{Å}`. The constant can be 0 for a rigid water molecule,
+    because the shape of the molecule will be preserved by the SHAKE algorithm
+    (see below) :cite:`ryckaert1977numerical, andersen1983rattle`.
+    Similarly, the angle coefficient for the H-O-H angle of the water
+    molecule sets the force constant of the angular harmonic potential to 0 and
+    the equilibrium angle to :math:`104.52^\circ`.
 
 ..  container:: justify
 
@@ -497,7 +490,7 @@ Energy minimization
 
     The *fix temp/berendsen* rescales the
     velocities of the atoms to force the temperature of the system
-    to reach the desired value of 1 K, and the shake algorithm
+    to reach the desired value of 1 K, and the SHAKE algorithm
     is used in order to maintain the shape of the water molecules.
 
 ..  container:: justify

sphinx/build/doctrees/environment.pickle

@@ -643,7 +643,7 @@ Using hydrid potentials
 
 ..  container:: justify
 
-    The shake algorithm is used to
+    The SHAKE algorithm is used to
     maintain the shape of the water molecules over time. Some of
     these features have been seen in previous tutorials.
 

sphinx/build/doctrees/non-tutorials/bibliography.doctree

@@ -311,7 +311,7 @@ <h2>Required software<a class="headerlink" href="#required-software" title="Link
 <h3>LAMMPS (2Aug2023)<a class="headerlink" href="#lammps-2aug2023" title="Link to this heading">¶</a></h3>
 <div class="justify docutils container">
 <p>Download and install LAMMPS version 2Aug2023 by following the
-instructions of the <a href="https://docs.lammps.org/Install.html" target="_blank">LAMMPS website</a> <span id="id1">[<a class="reference internal" href="bibliography.html#id16" title="Aidan P Thompson, H Metin Aktulga, Richard Berger, Dan S Bolintineanu, W Michael Brown, Paul S Crozier, Pieter J in't Veld, Axel Kohlmeyer, Stan G Moore, Trung Dac Nguyen, and others. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 271:108171, 2022.">1</a>]</span>.
+instructions of the <a href="https://docs.lammps.org/Install.html" target="_blank">LAMMPS website</a> <span id="id1">[<a class="reference internal" href="bibliography.html#id18" title="Aidan P Thompson, H Metin Aktulga, Richard Berger, Dan S Bolintineanu, W Michael Brown, Paul S Crozier, Pieter J in't Veld, Axel Kohlmeyer, Stan G Moore, Trung Dac Nguyen, and others. LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 271:108171, 2022.">1</a>]</span>.
 Depending on your operating system (i.e. Linux, macOS, or Windows),
 the procedure may differ.</p>
 </div>
@@ -337,7 +337,7 @@ <h3>LAMMPS (2Aug2023)<a class="headerlink" href="#lammps-2aug2023" title="Link t
 <h3>VMD (optional)<a class="headerlink" href="#vmd-optional" title="Link to this heading">¶</a></h3>
 <div class="justify docutils container">
 <p>To visualize the simulation, <a href="https://www.ks.uiuc.edu/Research/vmd" target="_blank">VMD</a> version 1.9.3 will
-be used <span id="id2">[<a class="reference internal" href="bibliography.html#id18" title="William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of molecular graphics, 14(1):33–38, 1996.">2</a>]</span>. Some basic instructions for VMD are given here in the
+be used <span id="id2">[<a class="reference internal" href="bibliography.html#id20" title="William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of molecular graphics, 14(1):33–38, 1996.">2</a>]</span>. Some basic instructions for VMD are given here in the
 <a class="reference internal" href="../tutorials/vmd/vmd-tutorial.html#vmd-label"><span class="std std-ref">VMD tutorial</span></a>. Feel free to use an alternative visualization
 software like <a href="https://www.ovito.org" target="_blank">Ovito</a>.</p>
 </div>
@@ -348,13 +348,13 @@ <h3>Python (optional)<a class="headerlink" href="#python-optional" title="Link t
 <p>To perform post-mortem analysis of the data during the <a class="reference internal" href="../tutorials/mdanalysis/mdanalysis-tutorial.html#mda-label"><span class="std std-ref">MDAnalysis tutorials</span></a>,
 MDAnalysis version 2.6.1 is used
 together with Python version 3.11.4
-<span id="id3">[<a class="reference internal" href="bibliography.html#id17" title="Guido Van Rossum and Fred L Drake Jr. Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam, 1995.">3</a>, <a class="reference internal" href="bibliography.html#id20" title="Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry, 32(10):2319–2327, 2011.">4</a>, <a class="reference internal" href="bibliography.html#id19" title="Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler JE Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, and others. MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th python in science conference, volume 98, 105. SciPy Austin, TX, 2016.">5</a>]</span>.</p>
+<span id="id3">[<a class="reference internal" href="bibliography.html#id19" title="Guido Van Rossum and Fred L Drake Jr. Python reference manual. Centrum voor Wiskunde en Informatica Amsterdam, 1995.">3</a>, <a class="reference internal" href="bibliography.html#id22" title="Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, and Oliver Beckstein. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of computational chemistry, 32(10):2319–2327, 2011.">4</a>, <a class="reference internal" href="bibliography.html#id21" title="Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler JE Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, and others. MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations. In Proceedings of the 15th python in science conference, volume 98, 105. SciPy Austin, TX, 2016.">5</a>]</span>.</p>
 </div>
 <div class="justify docutils container">
 <p>To plot the results from the simulations,
 <a href="https://matplotlib.org/3.5.3/api/_as_gen/matplotlib.pyplot.html" target="_blank">Matplotlib Pyplot</a> version 3.5.2 is used
 in combination with <a href="https://github.com/henriasv/lammps-logfile" target="_blank">lammps logfile</a>, a library allowing
-one to read the <em>log</em> file produced by LAMMPS <span id="id4">[<a class="reference internal" href="bibliography.html#id22" title="J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science &amp; Engineering, 9(3):90–95, 2007.">6</a>, <a class="reference internal" href="bibliography.html#id27" title="Henrik Andersen Sveinsson. LAMMPS logfile reader. 2021.">7</a>]</span>.</p>
+one to read the <em>log</em> file produced by LAMMPS <span id="id4">[<a class="reference internal" href="bibliography.html#id24" title="J. D. Hunter. Matplotlib: a 2d graphics environment. Computing in Science &amp; Engineering, 9(3):90–95, 2007.">6</a>, <a class="reference internal" href="bibliography.html#id29" title="Henrik Andersen Sveinsson. LAMMPS logfile reader. 2021.">7</a>]</span>.</p>
 </div>
 </section>
 <section id="text-editing-software">
@@ -379,14 +379,14 @@ <h2>Recommended reading<a class="headerlink" href="#recommended-reading" title="
 <div class="justify docutils container">
 <p>To better understand molecular dynamics simulations, I recommend the reading
 of <em>Understanding molecular simulation</em> by Daan Frenkel and Berend
-Smit <span id="id5">[<a class="reference internal" href="bibliography.html#id28" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">8</a>]</span>, as well as
+Smit <span id="id5">[<a class="reference internal" href="bibliography.html#id30" title="Daan Frenkel and Berend Smit. Understanding molecular simulation: from algorithms to applications. Elsevier, 2023.">8</a>]</span>, as well as
 <em>Computer simulation of liquids</em> by Michael Allen and Dominic Tildesley
-<span id="id6">[<a class="reference internal" href="bibliography.html#id14" title="Michael P Allen and Dominic J Tildesley. Computer simulation of liquids. Oxford university press, 2017.">9</a>]</span>. To understand the basic concepts
+<span id="id6">[<a class="reference internal" href="bibliography.html#id16" title="Michael P Allen and Dominic J Tildesley. Computer simulation of liquids. Oxford university press, 2017.">9</a>]</span>. To understand the basic concepts
 of fluid and Soft Matter systems, I recommend reading <em>Basic concepts for
 simple and complex liquids</em> by Jean-Louis Barrat and Jean-Pierre Hansen
 <span id="id7">[<a class="reference internal" href="bibliography.html#id2" title="Jean-Louis Barrat and Jean-Pierre Hansen. Basic concepts for simple and complex liquids. Cambridge University Press, 2003.">10</a>]</span>,
 as well as <em>Theory of simple liquids: with applications to soft matter</em>
-by Jean-Pierre Hansen and Ian Ranald McDonald <span id="id8">[<a class="reference internal" href="bibliography.html#id13" title="Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Academic press, 2013.">11</a>]</span>.</p>
+by Jean-Pierre Hansen and Ian Ranald McDonald <span id="id8">[<a class="reference internal" href="bibliography.html#id15" title="Jean-Pierre Hansen and Ian Ranald McDonald. Theory of simple liquids: with applications to soft matter. Academic press, 2013.">11</a>]</span>.</p>
 </div>
 </section>
 </section>