Merge pull request #77 from luciannahss/lu-sirah-doc

NAMD Folder

docs/source/AMBER/Tutorial-5.rst

@@ -44,7 +44,7 @@ The input file ``-i`` 1CRN.pqr contains the atomistic representation of `1CRN <h
 
 .. important::
 
-	By default charged termini are used, but it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”.
+	By default, charged termini are used, but it is possible to set them neutral by renaming the residues from **s**\[code\] to **a**\[code\] (Nt-acetylated) or **m**\[code\] (Ct-amidated) after mapping to CG, where \[code\] is the root residue name in SIRAH. For example, to set a neutral N-terminal Histidine protonated at epsilon nitrogen (:math:`N_{\epsilon}`) rename it from “sHe” to “aHe”.
 
 
 Please check both PDB and PQR structures using VMD:	

docs/source/AMBER/Tutorial-7.rst

@@ -35,7 +35,7 @@ The input file ``-i`` 2kyv.pqr contains the atomistic representation of `2KYV <h
 
 .. important::
 
-	If you already have an atomistic protein within a membrane, then you can simply map the entire system to SIRAH (this is highly recommended) and skip the step 2, however clipping the membrane patch may be required to set a correct solvation box (see bellow). By default no mapping is applied to lipids, as there is no standard naming convention for them. So users are requested to append a MAP file from the list in :ref:`Table 1 <table>`, by setting the flag ``-a`` in ``cgconv.pl``. We recommend using `PACKMOL <https://m3g.github.io/packmol/>`__ for building the system. Reference building-block structures are provided at folder ``sirah.amber/PDB/``, which agree with the mapping scheme ``sirah.amber/tools/CGCONV/maps/tieleman_lipid.map``. See :doc:`FAQs <../FAQ>` for cautions on mapping lipids to SIRAH and tips on using fragment-based topologies.  
+	If you already have an atomistic protein within a membrane, then you can simply map the entire system to SIRAH (this is highly recommended) and skip the step 2, however clipping the membrane patch may be required to set a correct solvation box (see bellow). By default, no mapping is applied to lipids, as there is no standard naming convention for them. So users are requested to append a MAP file from the list in :ref:`Table 1 <table>`, by setting the flag ``-a`` in ``cgconv.pl``. We recommend using `PACKMOL <https://m3g.github.io/packmol/>`__ for building the system. Reference building-block structures are provided at folder ``sirah.amber/PDB/``, which agree with the mapping scheme ``sirah.amber/tools/CGCONV/maps/tieleman_lipid.map``. See :doc:`FAQs <../FAQ>` for cautions on mapping lipids to SIRAH and tips on using fragment-based topologies.  
 
 .. tip::
 
@@ -154,7 +154,7 @@ Use a text editor to create the file ``gensystem.leap`` including the following
     saveAmberParmNetcdf ProtMem 2kyv_DMPC_cg.prmtop 2kyv_DMPC_cg.ncrst
     
     # EXIT
-quit
+    quit
 
 .. seealso::
 

docs/source/AMBER/installation.rst

@@ -11,7 +11,7 @@ Amber and AmberTools (version 16 or later) versions properly installed and runni
 
 .. tip::
 
-    `Download <https://ambermd.org/GetAmber.php#ambertools>`_ the lastest version of Amber and AmberTools and refer to the *How to obtain Amber23* section for more details on getting Amber23. In addition, go to the `Install Amber <https://ambermd.org/Installation.php>`_ page for specific instructions based on your operating system. If you have Amber already installed, it is unnecessary to install AmberTools separately.
+    `Download <https://ambermd.org/GetAmber.php#ambertools>`_ the latest version of Amber and AmberTools and refer to the *How to obtain Amber23* section for more details on getting Amber23. In addition, go to the `Install Amber <https://ambermd.org/Installation.php>`_ page for specific instructions based on your operating system. If you have Amber already installed, it is unnecessary to install AmberTools separately.
 
 
 **VMD**
@@ -48,7 +48,7 @@ Download `SIRAH for Amber <https://github.com/SIRAHFF/documentation/releases/tag
 
 .. code-block:: bash
 
-    tar -xzvf sirah_x2.3_24-07.amber.tar.gz 
+    tar -xzvf sirah_x2.3_24-07.amber.tar.gz
 
 If you are using a different version of SIRAH, type:
 
@@ -74,7 +74,7 @@ Create the following symbolic link in the folder tutorialX.X:
 
 .. code-block:: bash
 
-    ln -s ../sirah_x2.3_24-07.amber  sirah.amber
+    ln -s ../sirah_x2.3_24-07.amber sirah.amber
 
 .. note:: 
 
@@ -86,4 +86,4 @@ Create the following symbolic link in the folder tutorialX.X:
 
     Check the `AMBER Manual <https://ambermd.org/doc12/Amber23.pdf>`_ section **3.11.2** for more details. 
 
-    However, if you want the lastest parameters and implementations strongly advise you to use the developers version of SIRAH from GitHub. 
+    However, if you want the latest parameters and implementations strongly advise you to use the developers version of SIRAH from GitHub. 

docs/source/GROMACS/Tutorial-1.rst

@@ -201,7 +201,7 @@ ________________________
 
 .. important:: 
 
-	By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/1/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/1/CPU``.
+	By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/1/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/1/CPU``.
 
 The folder ``sirah.ff/tutorial/1/GPU/`` contains typical input files for energy minimization
 (``em_CGDNA.mdp``), equilibration (``eq_CGDNA.mdp``) and production (``md_CGDNA.mdp``) runs. Please
@@ -237,7 +237,7 @@ Make a new folder for the run:
 
 .. code-block:: bash 
 
-	gmx grompp -f ../sirah.ff/tutorial/1/GPU/eq_CGDNA.mdp -p ../topol.top -po eq.mdp -n ../dna_cg_ion.ndx -c dna_cg_em.gro -o dna_cg_eq.tpr 
+	gmx grompp -f ../sirah.ff/tutorial/1/GPU/eq_CGDNA.mdp -p ../topol.top -po eq.mdp -n ../dna_cg_ion.ndx -c dna_cg_em.gro -r dna_cg_em.gro -o dna_cg_eq.tpr 
 
 .. code-block:: bash 
 

docs/source/GROMACS/Tutorial-2.rst

@@ -185,7 +185,7 @@ ________________________
 
 .. important:: 
 
-	By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/2/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/2/CPU``.
+	By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/2/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/2/CPU``.
 
 The folder ``sirah.ff/tutorial/2/GPU/`` contains typical input files for energy minimization
 (``em_HYBSOL.mdp``), equilibration (``eq_HYBSOL.mdp``) and production (``md_HYBSOL.mdp``) runs. Please

docs/source/GROMACS/Tutorial-3.rst

@@ -65,7 +65,7 @@ When prompted, choose *SIRAH force field* and then *SIRAH solvent models*.
 
 .. note:: 
 
-	By default charged terminal are used, but it is possible to set them neutral with option ``-ter``.
+	By default, charged terminal are used, but it is possible to set them neutral with option ``-ter``.
 
 .. note::
 
@@ -268,7 +268,7 @@ ________________________
 
 .. important:: 
 
-	By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/3/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/3/CPU``.
+	By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/3/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/3/CPU``.
 
 The folder ``sirah.ff/tutorial/3/GPU/`` contains typical input files for energy minimization
 (``em1_CGPROT.mdp``, ``em2_CGPROT.mdp``), equilibration (``eq1_CGPROT.mdp``, ``eq2_CGPROT.mdp``)

docs/source/GROMACS/Tutorial-5.rst

@@ -210,7 +210,7 @@ ________________________
 
 .. important:: 
 
-	By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/5/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/5/CPU``.
+	By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/5/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/5/CPU``.
 
 The folder ``sirah.ff/tutorial/5/GPU/`` contains typical input files for energy minimization
 (``em_CGLIP.mdp``), equilibration (``eq_CGLIP.mdp``) and production (``md_CGLIP.mdp``) runs. Please

docs/source/GROMACS/Tutorial-6.rst

@@ -37,7 +37,7 @@ The input file ``-i`` 2kyv.pqr contains the atomistic representation of `2KYV <h
 
 .. important::
 
-	If you already have an atomistic protein within a membrane, then you can simply map the entire system to SIRAH (this is highly recommended) and skip the step of embedding the protein into a lipid bilayer, however clipping the membrane patch may be required to set a correct solvation box (see bellow). By default no mapping is applied to lipids, as there is no standard naming convention for them. So users are requested to append a MAP file from the list in :ref:`Table 1 <table>`, by setting the flag ``-a`` in ``cgconv.pl``. We recommend using `PACKMOL <https://m3g.github.io/packmol/>`__ for building the system. Reference building-block structures are provided at folder ``sirah.ff/PDB/``, which agree with the mapping scheme ``sirah.ff/tools/CGCONV/maps/tieleman_lipid.map``. See :doc:`FAQs <../FAQ>` for cautions on mapping lipids to SIRAH and tips on using fragment-based topologies.  
+	If you already have an atomistic protein within a membrane, then you can simply map the entire system to SIRAH (this is highly recommended) and skip the step of embedding the protein into a lipid bilayer, however clipping the membrane patch may be required to set a correct solvation box (see bellow). By default, no mapping is applied to lipids, as there is no standard naming convention for them. So users are requested to append a MAP file from the list in :ref:`Table 1 <table>`, by setting the flag ``-a`` in ``cgconv.pl``. We recommend using `PACKMOL <https://m3g.github.io/packmol/>`__ for building the system. Reference building-block structures are provided at folder ``sirah.ff/PDB/``, which agree with the mapping scheme ``sirah.ff/tools/CGCONV/maps/tieleman_lipid.map``. See :doc:`FAQs <../FAQ>` for cautions on mapping lipids to SIRAH and tips on using fragment-based topologies.  
 
 .. tip::
 
@@ -137,7 +137,7 @@ When prompted, choose *SIRAH force field* and then *SIRAH solvent models*.
 
 .. note:: 
 
-  By default charged terminal are used but it is possible to set them neutral with option ``-ter``
+  By default, charged terminal are used but it is possible to set them neutral with option ``-ter``
 
 .. note::
 
@@ -413,7 +413,7 @@ ________________________
 
 .. important:: 
 
-  By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/6/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/6/CPU``.
+  By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/6/GPU``). Example input files for using GROMACS on CPU can be found at: ``sirah.ff/tutorial/6/CPU``.
 
 The folder ``sirah.ff/tutorial/6/GPU/`` contains typical input files for energy minimization
 (``em1_CGLIPROT.mdp`` and ``em2_CGLIPROT.mdp``), equilibration (``eq1_CGLIPROT.mdp`` and ``eq2_CGLIPROT.mdp``) and production (``md_CGLIPROT.mdp``) runs. Please

docs/source/GROMACS/Tutorial-7.rst

@@ -110,7 +110,7 @@ In this specific case, the charge of the system is -5.000 e; this will be addres
 
 .. note:: 
 
-  By default charged terminal are used but it is possible to set them neutral with option ``-ter``.
+  By default, charged terminal are used but it is possible to set them neutral with option ``-ter``.
 
 .. note::
 
@@ -503,7 +503,7 @@ ________________________
 
 .. important:: 
 
-  By default in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/7/``). 
+  By default, in this tutorial we will use input files for GROMACS on GPU (``sirah.ff/tutorial/7/``). 
 
 The folder ``sirah.ff/tutorial/7/`` contains typical input files for energy minimization (``em1_CGPROT.mdp``, ``em2_CGPROT.mdp``, and ``em3_CGPROT.mdp``), equilibration (``eq1_CGPROT.mdp`` and ``eq2_CGPROT.mdp``), production (``md_CGPROT.mdp``) and SMD (``SMD_Force_CGPROT.mdp`` and ``SMD_Velocity_CGPROT.mdp``) runs. Please check carefully the input flags therein.
 

docs/source/GROMACS/installation-G.rst

@@ -7,7 +7,7 @@ __________________
 
 .. tip::
 
-	`Download <https://www.gromacs.org/Downloads>`_ the lastest version of GROMACS and check its `Installation Guide <https://manual.gromacs.org/documentation/current/install-guide/index.html>`_. 
+	`Download <https://www.gromacs.org/Downloads>`_ the latest version of GROMACS and check its `Installation Guide <https://manual.gromacs.org/documentation/current/install-guide/index.html>`_. 
 
 
 **VMD**

docs/source/NAMD/Appendix.rst

@@ -0,0 +1,18 @@
+Recompiling Namd
+________________________________
+
+If careful comparisons of the energies in NAMD and Amber are desired, the NAMD source code must be modified to use the same conversion factors, particularly to convert the electrostatic interactions to kcal/mol. These constants depend on the program:
+
+AMBER = 332.0522173
+CHARMM = 332.054
+NAMD = 332.0636
+
+To make the change, edit the line of the src/common.h file in the NAMD source code that contain
+
+#define COULOMB 332.0636
+
+to
+
+#define COULOMB 332.0522173
+
+Once this modification is made, recompile it and the program will be ready to run.