Merge pull request #66 from luciannahss/lu-sirah-doc

Update Background and Gromacs Tutorial 7

docs/source/Background SIRAH.rst

@@ -97,11 +97,11 @@ Available multiscale implementations in SIRAH:
 
 - An all-atoms/CG model covalently linking both resolutions within a nucleic acid chain (see [:ref:`13 <ref13>`]); 
 
-- A multiresolution solvent model allowing the mixture of fully atomistic solutes with a shell of atomistic solvent surrounded by CG water, applicable to highly solvated systems like viral capsids (see [:ref:`14 <ref14>`]).
+- A multiresolution solvent model allowing the mixture of fully atomistic solutes with a shell of atomistic solvent surrounded by CG water, applicable to highly solvated systems like viral capsids (see [:ref:`7 <ref7>`]).
 
-- A triple solvation scheme, treating water at all-atoms, CG, and supraCG levels, is also available (see [:ref:`14 <ref14>`]). 
+- A triple solvation scheme, treating water at all-atoms, CG, and supraCG levels, is also available (see [:ref:`7 <ref7>`]). 
 
-This is particularly useful for complex cellular systems and has been applied to assemble and simulate VLPs systems in an onion-shaped configuration using CG water (WT4) and supra-CG solvent (WLS) (**Figure 6**) (see [:ref:`10 <ref10>`] and [:ref:`14 <ref14>`]). 
+This is particularly useful for complex cellular systems and has been applied to assemble and simulate VLPs systems in an onion-shaped configuration using CG water (WT4) and supra-CG solvent (WLS) (**Figure 6**) (see [:ref:`7 <ref7>`] and [:ref:`10 <ref10>`]). 
 
 
 
@@ -268,15 +268,5 @@ References
    :alt: Citation
    :target: https://scholar.google.com/scholar?cites=5473055142318037579
 
-.. _ref14:
 
-[14] Machado, M. R.; González, H. C.; Pantano, S. MD Simulations of Virus like Particles with Supra CG Solvation Affordable to Desktop Computers. Journal of Chemical Theory and Computation 2017, 13, 5106–5116. |MC1| |MC1-cit|  
-
-.. |MC1| image:: https://img.shields.io/badge/DOI-10.1021%2Facs.jctc.7b00659-blue
-   :alt: Access the paper
-   :target: https://doi.org/10.1021/acs.jctc.7b00659
-
-.. |MC1-cit| image:: https://img.shields.io/endpoint?url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1021%2Facs.jctc.7b00659
-   :alt: Citation
-   :target: https://scholar.google.com/scholar?cites=16637391138490147245
 

docs/source/GROMACS/Tutorial-1.rst

@@ -83,19 +83,19 @@ these restraints edit ``topol.top`` to include the file ``WC_RST.itp`` at the en
      - Topology with WC restraints
    * - | ; Include Position restraint file
        | #ifdef POSRES
-       | #include "posre.itp"
+       | #include \"posre.itp\"
        | #endif
        | 
        | 
        |
        
      - | ; Include Position restraint file
        | #ifdef POSRES
-       | #include "posre.itp"
+       | #include \"posre.itp\"
        | #endif
        |
        | ; Watson-Crick restraints
-       | #include "./sirah.ff/tutorial/1/WC_RST.itp"
+       | #include \"./sirah.ff/tutorial/1/WC_RST.itp\"
 
 
 1.3. Solvate the system

docs/source/GROMACS/Tutorial-2.rst

@@ -36,14 +36,14 @@ For GROMACS to recognize SIRAH, edit your topology file ``topol.top`` adding the
    * - Topology before editing
      - Topology after editing
    * - | ; Include forcefield parameters 
-       | #include “amber99sb.ff/forcefield.itp” 
+       | #include \"amber99sb.ff/forcefield.itp\"
        |     
        |     
               
      - | ; Include forcefield parameters 
-       | #include “amber99sb.ff/forcefield.itp” 
-       | #include “./sirah.ff/hybsol_comb2.itp” 
-       | #include “./sirah.ff/solv.itp” 
+       | #include \"amber99sb.ff/forcefield.itp\"
+       | #include \"./sirah.ff/hybsol_comb2.itp\" 
+       | #include \"./sirah.ff/solv.itp\"
 
 
 .. important::

docs/source/GROMACS/Tutorial-3.rst

@@ -234,7 +234,7 @@ Add the restraints to ``topol.top``:
      - Topology after editing
    * - | ; Include Position restraint file
        | #ifdef POSRES
-       | #include "posre.itp"
+       | #include \"posre.itp\"
        | #endif
        
        | 
@@ -250,17 +250,17 @@ Add the restraints to ``topol.top``:
                   
      - | ; Include Position restraint file
        | #ifdef POSRES
-       | #include "posre.itp"
+       | #include \"posre.itp\"
        | #endif
         
        | ; Backbone restraints
        | #ifdef GN_GO
-       | #include "bkbres.itp"
+       | #include \"bkbres.itp\"
        | #endif
 	   
        | ; Backbone soft restrains
        | #ifdef GN_GO_SOFT
-       | #include "bkbres_soft.itp"
+       | #include \"bkbres_soft.itp\"
        | #endif
 
 3.4. Run the simulation
@@ -359,79 +359,3 @@ Now you can check the simulation using VMD:
     The file ``sirah_vmdtk.tcl`` is a Tcl script that is part of SIRAH Tools and contains the macros to properly visualize the coarse-grained structures in VMD. Use the command ``sirah-help`` in the Tcl/Tk console of VMD to access the manual pages. To learn about SIRAH Tools' capabilities, you can also go to the :ref:`SIRAH Tools tutorial <SIRAH tools>`.
 
 
-3.6. Calculate the solvent accessible surface (SAS)
-____________________________________________________
-
-Create the following symbolic link in the folder ``run/``:
-
-.. code-block:: bash 
-
-	ln -s ../sirah.ff/vdwradii.dat
-
-Calculate the SAS of the protein along the trajectory:
-
-.. code-block:: bash 
-
-	g_sas -s 1CRN_cg_md.tpr -f 1CRN_cg_md_pbc.xtc -n ../1CRN_cg_ion.ndx -qmax 0 -probe 0.21 -o area.xvg
-
-When prompted, choose *Protein* as both the group for calculation and the output.
-
-.. note:: 
-
-	The solvent probe radius corresponds to a WT4 bead while a charge of 0e refers to any
-	hydrophobic bead. The file ``vdwradii.dat`` must be placed at the same folder where *gmx sasa* is executed to assure that the correct van der Waals radii of SIRAH beads are used in the calculation.
-
-.. important:: 
-
-	*g_sas* is deprecated, the tool no longer automatically divides the surface into hydrophobic and hydrophilic areas, and there is no ``-f_index`` option. The same effects can be obtained by defining suitable selections for ``-output``. If you want output that contains the same numbers as with the old tool for a calculation group A and output group B, you can use `[1] <https://manual.gromacs.org/current/user-guide/cmdline.html>`_. ::
-
-	 gmx sasa -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"'
-
-
-Use Xmgrace to plot the results:
-
-.. code-block:: bash
-
-	xmgrace -nxy area.xvg
-
-..
-	3.7. Visualize the secondary structure
-	________________________________________
-
-
-	Load the processed trajectory in VMD::
-
-	vmd ../1CRN_cg_ion.psf ../1CRN_cg_ion.gro 1CRN_cg_md_pbc.xtc -e ../sirah.ff/tools/sirah_vmdtk.tcl
-
-	.. note::
-
-   The file ``sirah_vmdtk.tcl`` is a Tcl script that is part of SIRAH Tools and contains the macros to properly visualize the coarse-grained structures in VMD. Use the command ``sirah-help`` in the Tcl/Tk console of VMD to access the manual pages. To learn about SIRAH Tools' capabilities, you can also go to the :ref:`SIRAH Tools tutorial <SIRAH tools>`.
-
-	At the *Tk/Tcl console* run the command ``sirah_ss`` to get the secondary structure of the CG protein.
-
-	.. note:: 
-	
-	After assigning the secondary structure it is possible to represent a-helices with Bendix in VMD
-	1.9.2 or upper by setting the backbone particle name to GC (do not check the CG box).
-
-	To analyze the output files from ``sirah_ss``, go back at the shell command line and execute::
-
-	xmgrace -nxy ss_by_frame.xvg
-
-	.. code-block:: bash 
-
-	xmgrace -nxy ss_by_res.xvg
-
-	The file ss.mtx can be processed to visualize the time evolution of the secondary structure by residue::
-
-	../sirah.ff/tools/ssmtx2png.R --mtx=ss.mtx
-
-	.. code-block:: bash
-
-	display ssmtx.png
-
-	.. hint::
-
-	The usage of ssmtx2png.R can be accessed through::
-
-	../sirah.ff/tools/ssmtx2png.R --help

docs/source/GROMACS/Tutorial-6.rst

@@ -343,7 +343,7 @@ Edit each ``topol_Protein_chain_*.itp`` (A to E) to include the new position res
      - Topology after editing
    * - | ; Include Position restraint file 
        | #ifdef POSRES    
-       | #include "posre_Protein.itp" 
+       | #include \"posre_Protein.itp\" 
        | #endif
        |   
        |    
@@ -352,11 +352,11 @@ Edit each ``topol_Protein_chain_*.itp`` (A to E) to include the new position res
       
      - | ; Include Position restraint file 
        | #ifdef POSRES    
-       | #include "posre_Protein.itp" 
+       | #include \"posre_Protein.itp\" 
        | #endif
        |
        | #ifdef POSREBB    
-       | #include "posre_BB.itp" 
+       | #include \"posre_BB.itp\" 
        | #endif
 
 Use a similar procedure to set the positional restraints on lipid's phosphates.
@@ -392,7 +392,7 @@ Edit ``topol_Lipid_chain_F.itp`` to include the new position restraints and defi
      - Topology after editing
    * - | ; Include Position restraint file 
        | #ifdef POSRES    
-       | #include "posre_Lipid_chain_F.itp" 
+       | #include \"posre_Lipid_chain_F.itp\" 
        | #endif
        | 
        | 
@@ -401,11 +401,11 @@ Edit ``topol_Lipid_chain_F.itp`` to include the new position restraints and defi
               
      - | ; Include Position restraint file 
        | #ifdef POSRES    
-       | #include "posre_Lipid_chain_F.itp" 
+       | #include \"posre_Lipid_chain_F.itp\" 
        | #endif
        |
        | #ifdef POSREZ    
-       | #include "posre_Pz.itp" 
+       | #include \"posre_Pz.itp\" 
        | #endif
 
 6.5. Run the simulation