Refs #1 Added Panchao info

.gitignore

@@ -15,6 +15,7 @@
 !*.ipynb
 !*.jpeg
 !*.jpg
+!*.mdp
 !*.mol2
 !*.mpg
 !*.pbs

confinedBSA.ipynb

@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:bc78c2b4806e49f54419cc54a3066f84167b5605bf0bba722bc6b7c0ef1926ad"
+  "signature": "sha256:25c4d076fc3d45c8d35a9dac01a748bf9eb41f3da316e168bb245b7dcb0700d7"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -22,7 +22,7 @@
       "\n",
       "<a id='Simulations'></a><h3>Simulations</h3>\n",
       "<a href='#Simulations.gromacs_tutorial'>Gromacs tutorial for solvated Lyzosime</a>  \n",
-      "<a href='#Simulations.solvatedBSA'>Solvated BSA box</a>  \n",
+      "<a href='#Simulations.solvatedMBSA'>Solvated Monomeric BSA box</a>  \n",
       "<a href='#Simulations.silica'>Silica box</a>  \n",
       "<a href='#Simulations.protocol'>Protocol for initial configuration for confinedBSA</a>  \n",
       "\n",
@@ -64,14 +64,22 @@
       "\n",
       "Susceptibility plots:\n",
       "<center><table><tr>\n",
-      "<td>DBSA.jpg  <a href=\"files/experiment/Susceptibility_Dsilica_310K.JPG\"><img src=\"files/experiment/Susceptibility_Dsilica_310K.JPG\" width=\"100\"></a></td>  \n",
-      "<td>HBSA.jpg  <a href=\"files/experiment/Susceptibility_HBSA_310K.JPG\"><img src=\"files/experiment/Susceptibility_HBSA_310K.JPG\" width=\"100\"></a></td>\n",
+      "<td>DBSA  <a href=\"files/experiment/Susceptibility_Dsilica_310K.JPG\"><img src=\"files/experiment/Susceptibility_Dsilica_310K.JPG\" width=\"100\"></a></td>  \n",
+      "<td>HBSA  <a href=\"files/experiment/Susceptibility_HBSA_310K.JPG\"><img src=\"files/experiment/Susceptibility_HBSA_310K.JPG\" width=\"100\"></a></td>\n",
       "</tr></table></center>\n",
       "\n",
       "Comparison of MSD (label says 'Elastic Intensity' but it's wrong):  \n",
       "<center>SiO2_21A_3d_NoConnect.pdb  <a href=\"files/experiment/MSD_Dsilica_vs_HBSA_rebinned.jpg\"><img src=\"files/experiment/MSD_Dsilica_vs_HBSA_rebinned.jpg\" width=\"100\"></a></center>\n",
       "\n",
-      "Maximum MSD corresponds to ~0.4A, very minimal flucuation. Thus, there is very little deuterated water surrounding the protein in the silica-encapsulated DBSA sample.  "
+      "Maximum MSD corresponds to ~0.4A, very minimal flucuation. Thus, there is very little deuterated water surrounding the protein in the silica-encapsulated DBSA sample.  \n",
+      "\n",
+      "Slides that Panchao sent me providing more info on the samples:  \n",
+      "\n",
+      "<center><table><tr>\n",
+      "<td><a href=\"files/experiment/sample_manifest.png\"><img src=\"files/experiment/sample_manifest.png\" width=\"300\"></a></td>  \n",
+      "<td><a href=\"files/experiment/monomer_or_dimer.png\"><img src=\"files/experiment/monomer_or_dimer.png\" width=\"300\"></a></td>\n",
+      "<td><a href=\"files/experiment/hydration.png\"><img src=\"files/experiment/hydration.png\" width=\"300\"></a></td>\n",
+      "</tr></table></center>"
      ]
     },
     {
@@ -93,25 +101,56 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "(<a href='#Simulations'>Top</a>)<a id='Simulations.solvatedBSA'></a><h3>Solvated BSA box</h3>\n",
-      "In subdirectory <i>solvatedBSA</i>.  \n",
+      "(<a href='#Simulations'>Top</a>)<a id='Simulations.solvatedMBSA'></a><h3>Solvated Monomeric BSA box</h3>\n",
+      "In subdirectory <i>simulations/monomer/solvatedBSA</i>.  \n",
       "\n",
       "<b>Obtaining a working initial PDB file</b>:  \n",
       "Structure [3v03.pdb](http://www.rcsb.org/pdb/explore.do?structureId=3V03) is a dimer. We select the second chain:\n",
-      "<center><a href=\"files/simulation/solvatedBSA/3v03B_unclean.png\"><img src=\"files/simulation/solvatedBSA/3v03B_unclean.png\" width=\"100\"></a>  [3v03B_unclean.pdb](files/simulation/solvatedBSA/3v03B_unclean.pdb)</center>\n",
+      "<center><a href=\"files/simulation/monomer/solvatedBSA/3v03B_unclean.png\"><img src=\"files/simulation/monomer/solvatedBSA/3v03B_unclean.png\" width=\"100\"></a>  [3v03B_unclean.pdb](files/simulation/monomer/solvatedBSA/3v03B_unclean.pdb)</center>\n",
       "We clean up a bit the PDB file before obtaining the preprocessed Gromacs file.  \n",
       "- Removing crystallographic water Oxygen atoms.\n",
       "- Removing residue \"ACT\".  \n",
-      "- Submitting the PDB file to [pdb_hydro](http://lorentz.dynstr.pasteur.fr/pdb_hydro.php) server for generation of missing sidechains. We obtain structure [3v03B_noH.pdb](files/simulation/solvatedBSA/3v03B_noH.pdb) and log file [3v03B_PDB_Hydro.stdout](files/3v03B_PDB_Hydro.stdout). There are missing hydrogen atoms.\n",
+      "- Submitting the PDB file to [pdb_hydro](http://lorentz.dynstr.pasteur.fr/pdb_hydro.php) server for generation of missing sidechains. We obtain structure [3v03B_noH.pdb](files/simulation/monomer/solvatedBSA/3v03B_noH.pdb) and log file [3v03B_PDB_Hydro.stdout](files/simulation/monomer/solvatedBSA/3v03B_PDB_Hydro.stdout). There are missing hydrogen atoms.\n",
       "- Removed residues \"CA\" with residue numbers 584 to 586. These are not part of the BSA protein.\n",
-      "- Added hydrogens with command:  <code>gmx pdb2gmx -f 3v03B_noH.pdb -o 3v03B.pdb -p 3v03B.top -i 3v03B.itp -water spce -ff oplsaa &> 3v03B_pdb2gmx.log</code> to obtain [3v03B.pdb](files/simulation/solvatedBSA/3v03B.pdb), among other output files.\n",
+      "- Added hydrogens with command:  <code>gmx pdb2gmx -f 3v03B_noH.pdb -o 3v03B.pdb -p 3v03B.top -i 3v03B.itp -water spce -ff oplsaa &> 3v03B_pdb2gmx.log</code> to obtain [3v03B.pdb](files/simulation/monomer/solvatedBSA/3v03B.pdb), among other output files.\n",
       "\n",
+      "<b>Solvating the protein with water</b>:  \n",
       "Use OPLSAA force field and SPCE water model:  \n",
       "<code>gmx pdb2gmx -f 3v03B.pdb -o 3v03B.gro -p 3v03B.top -i 3v03B.itp -water spce -ff oplsaa &> 3v03B_pdb2gmx.log</code> outputs:  \n",
-      "- 3v03B_pdb2gmx.log states 579 residues, 9173 atoms, and a total charge of -16e. We will need 16Na atoms to neutralize.\n",
+      "- 3v03B_pdb2gmx.log states 579 residues, 9173 atoms, and a total charge of -16e. We need to place 16 Na atoms in order to neutralize the system.\n",
       "- 3v03B.gro processed binary gromacs file.\n",
       "- 3v03B.itp positional restraints file.\n",
-      "- 3v03B.top topology of the isolated molecule.\n"
+      "- 3v03B.top topology of the isolated molecule.\n",
+      "\n",
+      "The below command centers the protein in the box (-c), and places it at least 1.0 nm from the box edge (-d 1.0). The box type is defined as a cube (-bt cubic):  \n",
+      "<code>gmx editconf -f 3v03B.gro -o 3v03B_newbox.gro -c -d 1.0 -bt cubic</code>\n",
+      "\n",
+      "Fill with solvent (water). Solvation is accomplished using solvate:  \n",
+      "<code>cp 3v03B.top 3v03B_solv.top\n",
+      "<code>gmx solvate -cp 3v03B_newbox.gro -cs spc216.gro -o 3v03B_solv.gro -p 3v03B_solv.top -scale 0.8</code>\n",
+      "\n",
+      "Add ions:  \n",
+      "<code>cp 3v03B_solv.top 3v03B_solv_ions.top\n",
+      "gmx grompp -f ions.mdp -c 3v03B_solv.gro -p 3v03B_solv_ions.top -o ions.tpr\n",
+      "gmx genion -s ions.tpr -o 3v03B_solv_ions.gro -p 3v03B_solv_ions.top -neutral</code>  # select group number 13.\n",
+      "\n",
+      "<b>Minimize the protein</b>:  \n",
+      "(In subdirectory <i>simulation/monomer/solvatedBSA/minimize</i>)  \n",
+      "Minimize options specified in file [minimize.mdp](files/simulation/monomer/solvatedBSA/minimize/minimize.mdp).\n",
+      "<code>gmx grompp -f minimize.mdp -c 3v03B_solv_ions.gro -p 3v03B_solv_ions.top -o em.tpr</code> # creates binary input <code>em.tpr</code>.  \n",
+      "<code>gmx mdrun -v -deffnm em</code>\n",
+      "\n",
+      "<b>Relax the water around the protein</b>:  \n",
+      "(In subdirectory <i>simulation/monomer/solvatedBSA/minimize/relax</i>)  \n",
+      "50ps NVT run using restraints on the protein atoms. Coordinates defining the equilibrium positions for the restraints are in file <code>3v03B.itp</code>. This file is encoded in the topology file <code>3v03B_solv_ions.top</code>. Options for the run specified in file [relax_1.mdp](files/simulation/monomer/solvatedBSA/minimize/relax/relax_1.mdp).  \n",
+      "<code>gmx grompp -f relax_1.mdp -c em.gro -p 3v03B_solv_ions.top -o relax_1.tpr\n",
+      "gmx mdrun -ntpi 16 -pin on -deffnm relax_1</code>  # use 16 MPI threads, pin each thread to a diffeent core.\n",
+      "\n",
+      "Continue with a 1ns NPT run using restraints on the protein atoms. Input file is [relax_2.mdp](files/simulation/monomer/solvatedBSA/minimize/relax/relax_2.mdp).  \n",
+      "<code>gmx grompp -f relax_2.mdp -c relax_1.gro -t relax_1.cpt -p 3v03B_solv_ions.top -o relax_2.tpr\n",
+      "time gmx mdrun -ntmpi 16 -pin on -deffnm relax_2</code>\n",
+      "\n",
+      "\n"
      ]
     },
     {