Refs #1 changed directory for amorphous silica from MD

confinedBSA.ipynb

@@ -1,7 +1,7 @@
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@@ -24,7 +24,9 @@
       "<a href='#Simulations.references'>References</a>  \n",
       "<a href='#Simulations.gromacs_tutorial'>Gromacs tutorial for solvated Lyzosime</a>  \n",
       "<a href='#Simulations.solvatedMBSA'>Solvated Monomeric BSA box</a>  \n",
-      "<a href='#Simulations.silica'>Silica box</a>  \n",
+      "<a href='#Simulations.amorphous_from_MS'>Amorphous silica box from Materials Studio post</a>  \n",
+      "<a href='#Simulations.cristobalite'>Amorphous silica from cristobalite</a>  \n",
+      "\n",
       "<a href='#Simulations.protocol'>Protocol for initial configuration for confinedBSA</a>  \n",
       "\n",
       "<a id='meetings and reports'></a><b>Meetings</b>  \n",
@@ -205,7 +207,7 @@
       "</tr></table></center>  \n",
       "\n",
       "<b>Center protein in the simulation box</b>:  \n",
-      "<code>trjconv -f relax_2.cpt -s relax_2.tpr -pbc mol -ur compact -center -o relax_2_centered.gro -boxcenter tric</code>.\n",
+      "<code>gmx trjconv -f relax_2.cpt -s relax_2.tpr -pbc mol -ur compact -center -o relax_2_centered.gro -boxcenter tric</code>  \n",
       "- <code>Select group for centering: Group     1 (        Protein) has  9173 elements</code>  \n",
       "- <code>Select group for output: Group     0 (         System) has 84738 elements</code>  \n",
       "Produces file <code>relax_2_centered.gro</code>.  \n",
@@ -220,7 +222,7 @@
       "\n",
       "<code>close_solvent_atoms = group \"SOL\" and within 0.1874 of group \"Protein\";\n",
       "close_solvent_molecules = same resindex as close_solvent_atoms;\n",
-      "stripped_system = group \"Protein\" or close_solvent_molecules;</code>  \n",
+      "group \"Protein\" or close_solvent_molecules;</code>  \n",
       "\n",
       "We found a cutoff = 0.1874 to retain the 622 closest water molecules, simply by counting the number of lines containing \"SOL\" in file [stripped_system.pdb](files/simulation/monomer/solvatedBSA/minimize/relax/stripped_system.pdb) (see below).  \n",
       "\n",
@@ -234,15 +236,52 @@
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      "metadata": {},
      "source": [
-      "(<a href='#Simulations'>Top</a>)<a id='Simulations.silica'></a><h3>Silica box</h3>\n",
+      "(<a href='#Simulations'>Top</a>)<a id='Simulations.amorphous_from_MS'></a><h3>Amorphous silica box from Materials Studio post</h3>\n",
       "Issue [#4](https://github.com/jmborr/confinedBSA/issues/4)\n",
       "\n",
       "Silica $(SiO_2)_N$ has a sort-range order, whereby a Si atom is located at the center of a tetrahedron, whose vertices are defined by four O atoms.  \n",
-      "In subdirectory <i>silica</i> and also Materials Studio project <i>silica<i/> in virtual machine LEIOAVIRTUAL.  \n",
+      "\n",
+      "In subdirectory <i>silica/amorphous_from_md/</i> and also Materials Studio project <i>silica</i> in virtual machine LEIOAVIRTUAL.  \n",
       "I downloaded 21A box from a [post](https://community.3dsbiovia.com/Communities_Topics?id=90650000000L9G5AAK&name=Materials+Studio&tid=09a500000004QfAAAU#/feedtype=SINGLE_QUESTION_DETAIL) in the Materials Studio community].  \n",
-      "<center>SiO2_21A_3d_NoConnect.pdb  <a href=\"files/simulation/silica/SiO2_21A_3d_NoConnect.png\"><img src=\"files/simulation/silica/SiO2_21A_3d_NoConnect.png\" width=\"200\"></a></center>  \n",
+      "<center>SiO2_21A_3d_NoConnect.pdb  <a href=\"files/simulation/silica/amorphous_from_md/SiO2_21A_3d_NoConnect.png\"><img src=\"files/simulation/silica/amorphous_from_md/SiO2_21A_3d_NoConnect.png\" width=\"200\"></a></center>  \n",
       "Since the maximum diameter of BSA is ~77A, we use <i>SiO2_21A_3d_NoConnect.pdb</i> to create a 5x5x5 supercell of size ~107A. This precludes the protein from \"feeling itself\" via the periodic boundary conditions.  \n",
-      "<center>SiO2_107A_3d_NoConnect.pdb  <a href=\"files/simulation/silica/SiO2_107A_3d_NoConnect.png\"><img src=\"files/simulation/silica/SiO2_107A_3d_NoConnect.png\" width=\"200\"></a><center>  \n"
+      "<center>SiO2_107A_3d_NoConnect.pdb  <a href=\"files/simulation/silica/amorphous_from_md/SiO2_107A_3d_NoConnect.png\"><img src=\"files/simulation/silica/amorphous_from_md/SiO2_107A_3d_NoConnect.png\" width=\"200\"></a><center>  \n",
+      "\n",
+      "<b>Inserting the protein in the silica box</b>:  \n"
+     ]
+    },
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "(<a href='#Simulations'>Top</a>)<a id='Simulations.cristobalite'></a><h3>Amorphous silica from cristobalite</h3>\n",
+      "\n",
+      "From the [Crystallography Open Database](http://www.crystallography.net/cod/search.html) we search for the crystal structure of alpha-cristobalite, one of the morphologies of $SiO_2$:  \n",
+      "\n",
+      "<center>SiO2_107A_3d_NoConnect.pdb  <a href=\"files/simulation/silica/cristobalite/cristobalite_search.png\"><img src=\"files/simulation/silica/cristobalite/cristobalite_search.png\" width=\"300\"></a></center>  \n",
+      "\n",
+      "In Materials studio, the supercell replicating the unit cell 21 times along X and Y and 15 times along Z is able to surround BSA.  \n",
+      "\n",
+      "<center><a href=\"files/simulation/silica/cristobalite/cristobalite_21_21_15.gif\"><img src=\"files/simulation/silica/cristobalite/cristobalite_21_21_15.gif\" width=\"200\"></a>  [cristobalite_21_21_15.pdb](files/simulation/silica/cristobalite/cristobalite_21_21_15.pdb)</center>  \n",
+      "\n",
+      "A post in materials studio prescribes a recipe to build amorphous silica starting with the <code>amorphous cell</code> module. We can take parts of this recipe to create amorphous silica from a cristobalite supercell.  \n",
+      "\n",
+      "<pre>From: Jason DeJoannis\n",
+      "I think we built that structure in partnership with Corning. It is documented in this paper:\n",
+      "Vyas, Dickinson and Armstrong-Poston, Mol Sim, 32, 2, 135 (2006).\n",
+      "\n",
+      "Build bulk glass with Amorphous Cell\n",
+      "Pack cell with SiO2 and Si2O4 fragments at density of 2g/mL\n",
+      "cvff_aug forcefield with Ewald\n",
+      "Anneal the bulk\n",
+      "NVT at 7000K for 20ps\n",
+      "NPT for 20ps\n",
+      "Reduce T in 1000K increments with 20ps at each temperature down to 300K\n",
+      "Create the surface\n",
+      "Cleave and add vacuum slab 50-60A\n",
+      "Extend surface supercell as needed\n",
+      "Anneal the surface\n",
+      "Start at 600K and cool to 300K in steps of 100</pre>"
      ]
     },
     {