NAMD Tutorial 1 and grammar fix

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**
@@ -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

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
@@ -195,7 +195,7 @@ Create an index files adding a group for WT4 and NaW:
 
 .. code-block:: bash
 
-	echo -e "r WT4 | r NaW\nq\n" | make_ndx -f dna_ion.gro -o dna_ion.ndx
+	echo -e "r WT4 | r NaW\nq\n" | gmx make_ndx -f dna_ion.gro -o dna_ion.ndx
 
 .. note::
 
@@ -215,17 +215,17 @@ Make a new folder for the run:
 
 .. code-block:: bash
 
-	mdrun -deffnm dna_em &> EM.log &
+	gmx mdrun -deffnm dna_em &> EM.log &
 
 **Equilibration**:
 
 .. code-block:: bash 
 
-	gmx grompp -f ../sirah.ff/tutorial/2/GPU/eq_HYBSOL.mdp -p ../topol.top -po eq.mdp -n ../dna_ion.ndx -c dna_em.gro -o dna_eq.tpr 
+	gmx grompp -f ../sirah.ff/tutorial/2/GPU/eq_HYBSOL.mdp -p ../topol.top -po eq.mdp -n ../dna_ion.ndx -c dna_em.gro -r dna_em.gro -o dna_eq.tpr 
 
 .. code-block:: bash 
 
-	mdrun -deffnm dna_eq &> EQ.log &
+	gmx mdrun -deffnm dna_eq &> EQ.log &
 
 **Production (100ns)**:
 
@@ -235,7 +235,7 @@ Make a new folder for the run:
 
 .. code-block:: bash
 
-	mdrun -deffnm dna_md &> MD.log &
+	gmx mdrun -deffnm dna_md &> MD.log &
 
 .. note::
 

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-4.rst

@@ -18,7 +18,7 @@ Map the atomistic structure of the closed circular DNA to its CG representation:
 
 .. code-block:: bash
 
-	./sirah.ff/tools/CGCONV/cgconv.pl -i sirah.ff/tutorial/4/ccdna.pdb | sed -e 's/DCX A 1/CW5 A 1/' -e 's/DCX B 1/CW5 B 1/' > ccdna_cg.pdb
+	./sirah.ff/tools/CGCONV/cgconv.pl -i sirah.ff/tutorial/4/ccdna.pdb | sed -e 's/DCX A   1/CW5 A   1/' -e 's/DCX B   1/CW5 B   1/' > ccdna_cg.pdb
 
 The input file ``-i`` ccdna.pdb contains all the heavy atoms composing the DNA molecule, while the output ``-o`` ccdna_cg.pdb preserves a few of them.
 
@@ -207,17 +207,17 @@ Make a new folder for the run:
 
 .. code-block:: bash
 
-	mdrun -deffnm ccdna_cg_em &> EM.log &
+	gmx mdrun -deffnm ccdna_cg_em &> EM.log &
 
 **Equilibration**:
 
 .. code-block:: bash 
 
-	gmx grompp -f ../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp -p ../topol.top -po eq.mdp -n ../ccdna_cg_ion.ndx -c ccdna_cg_em.gro -o ccdna_cg_eq.tpr 
+	gmx grompp -f ../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp -p ../topol.top -po eq.mdp -n ../ccdna_cg_ion.ndx -c ccdna_cg_em.gro -r ccdna_cg_em.gro -o ccdna_cg_eq.tpr 
 
 .. code-block:: bash 
 
-	mdrun -deffnm ccdna_cg_eq &> EQ.log &
+	gmx mdrun -deffnm ccdna_cg_eq &> EQ.log &
 
 **Production (100ns)**:
 
@@ -227,7 +227,7 @@ Make a new folder for the run:
 
 .. code-block:: bash
 
-	mdrun -deffnm ccdna_cg_md &> MD.log &
+	gmx mdrun -deffnm ccdna_cg_md &> MD.log &
 
 .. note::
 
@@ -254,4 +254,4 @@ Now you can check the simulation using VMD:
 
 .. 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>`.
+    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>`.

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.