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luciannahss committed Dec 13, 2024
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14 changes: 9 additions & 5 deletions NAMD/Tutorial-1.html
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Expand Up @@ -244,7 +244,7 @@ <h1>1.4. Create Backbone and Protein restraints<a class="headerlink" href="#crea
</pre></div>
</div>
<p>Run the VMD script to generate the pdb restriction file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-dispdev<span class="w"> </span>text<span class="w"> </span>–e<span class="w"> </span>restraints.tcl
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-dispdev<span class="w"> </span>text<span class="w"> </span>-e<span class="w"> </span>restraints.tcl
</pre></div>
</div>
</section>
Expand All @@ -257,7 +257,7 @@ <h2>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
</pre></div>
</div>
<p>Copy the input files to the folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>sirah.amber/tutorial/NAMD/1/NAMD2/*.conf<span class="w"> </span>.
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf<span class="w"> </span>.
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/NAMD/1/NAMD2</span></code> contains typical input files for energy minimization (<code class="docutils literal notranslate"><span class="pre">em1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">em2.conf</span></code>), heating (<code class="docutils literal notranslate"><span class="pre">heat.conf</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2.conf</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md.conf</span></code>) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.</p>
Expand Down Expand Up @@ -319,12 +319,16 @@ <h2>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
</section>
<section id="namd3">
<h2>1.5.2 NAMD3<a class="headerlink" href="#namd3" title="Link to this heading"></a></h2>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.</p>
</div>
<p>Make a new folder for the run:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>-p<span class="w"> </span>run<span class="p">;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>run
</pre></div>
</div>
<p>Copy the input files to the folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>sirah.amber/tutorial/NAMD/1/NAMD3/*.conf<span class="w"> </span>.
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf<span class="w"> </span>.
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/NAMD/1/NAMD3</span></code> contains typical input files for energy minimization (<code class="docutils literal notranslate"><span class="pre">em1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">em2.conf</span></code>), heating (<code class="docutils literal notranslate"><span class="pre">heat.conf</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2.conf</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md.conf</span></code>) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.</p>
Expand Down Expand Up @@ -532,7 +536,7 @@ <h2>1.7.4 Equilibration<a class="headerlink" href="#equilibration" title="Link t
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp"># </span>Constraints<span class="w"> </span>of<span class="w"> </span>protein
<span class="go">if {1} { ;# If 1 read the block</span>
<span class="go">constraints on ;# Turns on constraints</span>
<span class="go">consref your_restraints.pdb ;# Reference PDB file for constraint positions</span>
<span class="go">consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)</span>
<span class="go">conskfile your_restraints.pdb ;# File containing constraint force constants</span>
<span class="go">constraintScaling 1 ;# Scaling factor for constraint forces</span>
<span class="go">consexp 2 ;# Exponent for constraint potential</span>
Expand All @@ -547,7 +551,7 @@ <h2>1.7.4 Equilibration<a class="headerlink" href="#equilibration" title="Link t
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp"># </span>Constraints<span class="w"> </span>of<span class="w"> </span>protein
<span class="go">if {1} { ;# If 1 read the block</span>
<span class="go">constraints on ;# Turns on constraints</span>
<span class="go">consref your_restraints.pdb ;# Reference PDB file for constraint positions</span>
<span class="go">consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)</span>
<span class="go">conskfile your_restraints.pdb ;# File containing constraint force constants</span>
<span class="go">constraintScaling 0.1 ;# Scaling factor for constraint forces</span>
<span class="go">consexp 2 ;# Exponent for constraint potential</span>
Expand Down
14 changes: 9 additions & 5 deletions Tutorials namd.html
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Expand Up @@ -359,7 +359,7 @@ <h3>1.4. Create Backbone and Protein restraints<a class="headerlink" href="#crea
</pre></div>
</div>
<p>Run the VMD script to generate the pdb restriction file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-dispdev<span class="w"> </span>text<span class="w"> </span>–e<span class="w"> </span>restraints.tcl
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>vmd<span class="w"> </span>-dispdev<span class="w"> </span>text<span class="w"> </span>-e<span class="w"> </span>restraints.tcl
</pre></div>
</div>
</section>
Expand All @@ -372,7 +372,7 @@ <h4>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
</pre></div>
</div>
<p>Copy the input files to the folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>sirah.amber/tutorial/NAMD/1/NAMD2/*.conf<span class="w"> </span>.
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf<span class="w"> </span>.
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/NAMD/1/NAMD2</span></code> contains typical input files for energy minimization (<code class="docutils literal notranslate"><span class="pre">em1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">em2.conf</span></code>), heating (<code class="docutils literal notranslate"><span class="pre">heat.conf</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2.conf</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md.conf</span></code>) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.</p>
Expand Down Expand Up @@ -434,12 +434,16 @@ <h4>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
</section>
<section id="namd3">
<h4>1.5.2 NAMD3<a class="headerlink" href="#namd3" title="Link to this heading"></a></h4>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.</p>
</div>
<p>Make a new folder for the run:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>-p<span class="w"> </span>run<span class="p">;</span><span class="w"> </span><span class="nb">cd</span><span class="w"> </span>run
</pre></div>
</div>
<p>Copy the input files to the folder:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>sirah.amber/tutorial/NAMD/1/NAMD3/*.conf<span class="w"> </span>.
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>cp<span class="w"> </span>../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf<span class="w"> </span>.
</pre></div>
</div>
<p>The folder <code class="docutils literal notranslate"><span class="pre">sirah.amber/tutorial/NAMD/1/NAMD3</span></code> contains typical input files for energy minimization (<code class="docutils literal notranslate"><span class="pre">em1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">em2.conf</span></code>), heating (<code class="docutils literal notranslate"><span class="pre">heat.conf</span></code>), equilibration (<code class="docutils literal notranslate"><span class="pre">eq1.conf</span></code> and <code class="docutils literal notranslate"><span class="pre">eq2.conf</span></code>) and production (<code class="docutils literal notranslate"><span class="pre">md.conf</span></code>) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.</p>
Expand Down Expand Up @@ -647,7 +651,7 @@ <h4>1.7.4 Equilibration<a class="headerlink" href="#equilibration" title="Link t
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp"># </span>Constraints<span class="w"> </span>of<span class="w"> </span>protein
<span class="go">if {1} { ;# If 1 read the block</span>
<span class="go">constraints on ;# Turns on constraints</span>
<span class="go">consref your_restraints.pdb ;# Reference PDB file for constraint positions</span>
<span class="go">consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)</span>
<span class="go">conskfile your_restraints.pdb ;# File containing constraint force constants</span>
<span class="go">constraintScaling 1 ;# Scaling factor for constraint forces</span>
<span class="go">consexp 2 ;# Exponent for constraint potential</span>
Expand All @@ -662,7 +666,7 @@ <h4>1.7.4 Equilibration<a class="headerlink" href="#equilibration" title="Link t
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp"># </span>Constraints<span class="w"> </span>of<span class="w"> </span>protein
<span class="go">if {1} { ;# If 1 read the block</span>
<span class="go">constraints on ;# Turns on constraints</span>
<span class="go">consref your_restraints.pdb ;# Reference PDB file for constraint positions</span>
<span class="go">consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)</span>
<span class="go">conskfile your_restraints.pdb ;# File containing constraint force constants</span>
<span class="go">constraintScaling 0.1 ;# Scaling factor for constraint forces</span>
<span class="go">consexp 2 ;# Exponent for constraint potential</span>
Expand Down
14 changes: 9 additions & 5 deletions _sources/NAMD/Tutorial-1.rst.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ Run the VMD script to generate the pdb restriction file:

.. code-block:: bash
vmd -dispdev text –e restraints.tcl
vmd -dispdev text -e restraints.tcl
1.5. Run the simulation
Expand All @@ -218,7 +218,7 @@ Copy the input files to the folder:

.. code-block:: bash
cp sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
cp ../sirah.amber/tutorial/NAMD/1/NAMD2/*.conf .
The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

Expand Down Expand Up @@ -300,6 +300,10 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files fo
1.5.2 NAMD3
~~~~~~~~~~~~~

.. warning::

Point release 3.0.1 fixes potentially impactful bugs in 3.0. All users are strongly encouraged to upgrade to this version.

Make a new folder for the run:

.. code-block:: bash
Expand All @@ -310,7 +314,7 @@ Copy the input files to the folder:

.. code-block:: bash
cp sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
cp ../sirah.amber/tutorial/NAMD/1/NAMD3/*.conf .
The folder ``sirah.amber/tutorial/NAMD/1/NAMD3`` contains typical input files for energy minimization (``em1.conf`` and ``em2.conf``), heating (``heat.conf``), equilibration (``eq1.conf`` and ``eq2.conf``) and production (``md.conf``) runs. Please carefully review the input files, paying especially attention to the cell dimension values, names, and restrictions.

Expand Down Expand Up @@ -559,7 +563,7 @@ For ``eq1.conf``:
# Constraints of protein
if {1} { ;# If 1 read the block
constraints on ;# Turns on constraints
consref your_restraints.pdb ;# Reference PDB file for constraint positions
consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)
conskfile your_restraints.pdb ;# File containing constraint force constants
constraintScaling 1 ;# Scaling factor for constraint forces
consexp 2 ;# Exponent for constraint potential
Expand All @@ -577,7 +581,7 @@ For ``eq2.conf``:
# Constraints of protein
if {1} { ;# If 1 read the block
constraints on ;# Turns on constraints
consref your_restraints.pdb ;# Reference PDB file for constraint positions
consref your_restraints.coor ;# Reference PDB file for the last position (last_step.coor)
conskfile your_restraints.pdb ;# File containing constraint force constants
constraintScaling 0.1 ;# Scaling factor for constraint forces
consexp 2 ;# Exponent for constraint potential
Expand Down
10 changes: 7 additions & 3 deletions _static/js/versions.js
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@@ -1,17 +1,21 @@
const themeFlyoutDisplay = "hidden";
const themeVersionSelector = "True";
const themeLanguageSelector = "True";
const themeVersionSelector = true;
const themeLanguageSelector = true;

if (themeFlyoutDisplay === "attached") {
function renderLanguages(config) {
if (!config.projects.translations.length) {
return "";
}

// Insert the current language to the options on the selector
let languages = config.projects.translations.concat(config.projects.current);
languages = languages.sort((a, b) => a.language.name.localeCompare(b.language.name));

const languagesHTML = `
<dl>
<dt>Languages</dt>
${config.projects.translations
${languages
.map(
(translation) => `
<dd ${translation.slug == config.projects.current.slug ? 'class="rtd-current-item"' : ""}>
Expand Down
2 changes: 1 addition & 1 deletion searchindex.js
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