deploy: 359477c

GROMACS/Tutorial-4.html

@@ -102,7 +102,7 @@
 <section id="build-cg-representations">
 <h1>4.1. Build CG representations<a class="headerlink" href="#build-cg-representations" title="Link to this heading"></a></h1>
 <p>Map the atomistic structure of the closed circular DNA to its CG representation:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.ff/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>sirah.ff/tutorial/4/ccdna.pdb<span class="w"> </span><span class="p">|</span><span class="w"> </span>sed<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX A 1/CW5 A 1/&#39;</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX B 1/CW5 B 1/&#39;</span><span class="w"> </span>&gt;<span class="w"> </span>ccdna_cg.pdb
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.ff/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>sirah.ff/tutorial/4/ccdna.pdb<span class="w"> </span><span class="p">|</span><span class="w"> </span>sed<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX A   1/CW5 A   1/&#39;</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX B   1/CW5 B   1/&#39;</span><span class="w"> </span>&gt;<span class="w"> </span>ccdna_cg.pdb
 </pre></div>
 </div>
 <p>The input file <code class="docutils literal notranslate"><span class="pre">-i</span></code> ccdna.pdb contains all the heavy atoms composing the DNA molecule, while the output <code class="docutils literal notranslate"><span class="pre">-o</span></code> ccdna_cg.pdb preserves a few of them.</p>
@@ -266,21 +266,21 @@ <h1>4.4. Run the simulation<a class="headerlink" href="#run-the-simulation" titl
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/em_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>em.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>../ccdna_cg_ion.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_em.tpr
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_em<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EM.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_em<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EM.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <p><strong>Equilibration</strong>:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>eq.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_eq.tpr
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>eq.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-r<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_eq.tpr
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_eq<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EQ.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_eq<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EQ.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <p><strong>Production (100ns)</strong>:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/md_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>md.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_eq.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_md.tpr<span class="w"> </span>mdrun
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_md<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>MD.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_md<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>MD.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <div class="admonition note">

Tutorials gromacs.html

@@ -1086,7 +1086,7 @@ <h3>3.5. Visualizing the simulation<a class="headerlink" href="#id23" title="Lin
 <section id="id29">
 <h3>4.1. Build CG representations<a class="headerlink" href="#id29" title="Link to this heading"></a></h3>
 <p>Map the atomistic structure of the closed circular DNA to its CG representation:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.ff/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>sirah.ff/tutorial/4/ccdna.pdb<span class="w"> </span><span class="p">|</span><span class="w"> </span>sed<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX A 1/CW5 A 1/&#39;</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX B 1/CW5 B 1/&#39;</span><span class="w"> </span>&gt;<span class="w"> </span>ccdna_cg.pdb
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./sirah.ff/tools/CGCONV/cgconv.pl<span class="w"> </span>-i<span class="w"> </span>sirah.ff/tutorial/4/ccdna.pdb<span class="w"> </span><span class="p">|</span><span class="w"> </span>sed<span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX A   1/CW5 A   1/&#39;</span><span class="w"> </span>-e<span class="w"> </span><span class="s1">&#39;s/DCX B   1/CW5 B   1/&#39;</span><span class="w"> </span>&gt;<span class="w"> </span>ccdna_cg.pdb
 </pre></div>
 </div>
 <p>The input file <code class="docutils literal notranslate"><span class="pre">-i</span></code> ccdna.pdb contains all the heavy atoms composing the DNA molecule, while the output <code class="docutils literal notranslate"><span class="pre">-o</span></code> ccdna_cg.pdb preserves a few of them.</p>
@@ -1250,21 +1250,21 @@ <h3>4.4. Run the simulation<a class="headerlink" href="#id33" title="Link to thi
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/em_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>em.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>../ccdna_cg_ion.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_em.tpr
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_em<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EM.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_em<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EM.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <p><strong>Equilibration</strong>:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>eq.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_eq.tpr
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/eq_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>eq.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-r<span class="w"> </span>ccdna_cg_em.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_eq.tpr
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_eq<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EQ.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_eq<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>EQ.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <p><strong>Production (100ns)</strong>:</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>grompp<span class="w"> </span>-f<span class="w"> </span>../sirah.ff/tutorial/4/GPU/md_CGDNA.mdp<span class="w"> </span>-p<span class="w"> </span>../topol.top<span class="w"> </span>-po<span class="w"> </span>md.mdp<span class="w"> </span>-n<span class="w"> </span>../ccdna_cg_ion.ndx<span class="w"> </span>-c<span class="w"> </span>ccdna_cg_eq.gro<span class="w"> </span>-o<span class="w"> </span>ccdna_cg_md.tpr<span class="w"> </span>mdrun
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_md<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>MD.log<span class="w"> </span><span class="p">&amp;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>gmx<span class="w"> </span>mdrun<span class="w"> </span>-deffnm<span class="w"> </span>ccdna_cg_md<span class="w"> </span><span class="p">&amp;</span>&gt;<span class="w"> </span>MD.log<span class="w"> </span><span class="p">&amp;</span>
 </pre></div>
 </div>
 <div class="admonition note">

_sources/GROMACS/Tutorial-4.rst.txt

@@ -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>`.