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1 change: 1 addition & 0 deletions Developers.html
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Expand Up @@ -103,6 +103,7 @@ <h2>Developers<a class="headerlink" href="#id1" title="Link to this heading">
<li><p>Martín Soñora</p></li>
<li><p>Lucianna Silva dos Santos</p></li>
<li><p>Andres Ballesteros</p></li>
<li><p>Antonella Alba</p></li>
<li><p>Ezequiel N. Frigini</p></li>
<li><p>Matias Machado</p></li>
<li><p>Pablo Garay</p></li>
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10 changes: 9 additions & 1 deletion NAMD/Tutorial-1.html
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Expand Up @@ -94,7 +94,7 @@
<p>Please report bugs, errors or enhancement requests through <a class="reference external" href="https://github.com/SIRAHFF/documentation/issues">Issue Tracker</a> or if you have a question about SIRAH open a <a class="reference external" href="https://github.com/SIRAHFF/documentation/discussions">New Discussion</a>.</p>
</div>
<p>This tutorial shows how to use the SIRAH force field to perform a coarse grained (CG) simulation of a protein in explicit solvent (called WatFour, WT4). The main references for
this tutorial are: <a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/ct100379f">Darré et al.</a>, <a class="reference external" href="https://doi.org/10.1021/acs.jctc.9b00006">Machado et al.</a> and <a class="reference external" href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">Machado &amp; Pantano</a>. We strongly advise you to read these articles before starting the tutorial.</p>
this tutorial are: <a class="reference external" href="https://doi.org/10.1021/acs.jpcb.4c03278">Cantero et al.</a>, <a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/ct100379f">Darré et al.</a>, <a class="reference external" href="https://doi.org/10.1021/acs.jctc.9b00006">Machado et al.</a> and <a class="reference external" href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">Machado &amp; Pantano</a>. We strongly advise you to read these articles before starting the tutorial.</p>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>Check the <a class="reference internal" href="../Tutorials%20amber.html#download-amber"><span class="std std-ref">Setting up SIRAH</span></a> section for download and set up details before starting this tutorial.
Expand Down Expand Up @@ -302,6 +302,10 @@ <h2>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
<p class="admonition-title">Note</p>
<p>In this stage, the restriction file <code class="docutils literal notranslate"><span class="pre">prot_restraints.pdb</span></code> is assigned to the consref and conskfile flags.</p>
</div>
<p><strong>Solvent equilibration (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd2<span class="w"> </span>+p8<span class="w"> </span>eq1.conf<span class="w"> </span>&gt;<span class="w"> </span>eq1.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Soft equilibration to improve side chain solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd2<span class="w"> </span>+p8<span class="w"> </span>eq2.conf<span class="w"> </span>&gt;<span class="w"> </span>eq2.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
Expand Down Expand Up @@ -375,6 +379,10 @@ <h2>1.5.2 NAMD3<a class="headerlink" href="#namd3" title="Link to this heading">
<p class="admonition-title">Note</p>
<p>In this stage, the restriction file <code class="docutils literal notranslate"><span class="pre">prot_restraints.pdb</span></code> is assigned to the consref and conskfile flags.</p>
</div>
<p><strong>Solvent equilibration (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd3<span class="w"> </span>+p4<span class="w"> </span>eq1.conf<span class="w"> </span>&gt;<span class="w"> </span>eq1.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Soft equilibration to improve side chain solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd3<span class="w"> </span>+p4<span class="w"> </span>eq2.conf<span class="w"> </span>&gt;<span class="w"> </span>eq2.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
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10 changes: 9 additions & 1 deletion Tutorials namd.html
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Expand Up @@ -209,7 +209,7 @@ <h3>Download and Setting up SIRAH<a class="headerlink" href="#download-and-setti
<p>Please report bugs, errors or enhancement requests through <a class="reference external" href="https://github.com/SIRAHFF/documentation/issues">Issue Tracker</a> or if you have a question about SIRAH open a <a class="reference external" href="https://github.com/SIRAHFF/documentation/discussions">New Discussion</a>.</p>
</div>
<p>This tutorial shows how to use the SIRAH force field to perform a coarse grained (CG) simulation of a protein in explicit solvent (called WatFour, WT4). The main references for
this tutorial are: <a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/ct100379f">Darré et al.</a>, <a class="reference external" href="https://doi.org/10.1021/acs.jctc.9b00006">Machado et al.</a> and <a class="reference external" href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">Machado &amp; Pantano</a>. We strongly advise you to read these articles before starting the tutorial.</p>
this tutorial are: <a class="reference external" href="https://doi.org/10.1021/acs.jpcb.4c03278">Cantero et al.</a>, <a class="reference external" href="https://pubs.acs.org/doi/abs/10.1021/ct100379f">Darré et al.</a>, <a class="reference external" href="https://doi.org/10.1021/acs.jctc.9b00006">Machado et al.</a> and <a class="reference external" href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">Machado &amp; Pantano</a>. We strongly advise you to read these articles before starting the tutorial.</p>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>Check the <a class="reference internal" href="Tutorials%20amber.html#download-amber"><span class="std std-ref">Setting up SIRAH</span></a> section for download and set up details before starting this tutorial.
Expand Down Expand Up @@ -417,6 +417,10 @@ <h4>1.5.1 NAMD2<a class="headerlink" href="#namd2" title="Link to this heading">
<p class="admonition-title">Note</p>
<p>In this stage, the restriction file <code class="docutils literal notranslate"><span class="pre">prot_restraints.pdb</span></code> is assigned to the consref and conskfile flags.</p>
</div>
<p><strong>Solvent equilibration (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd2<span class="w"> </span>+p8<span class="w"> </span>eq1.conf<span class="w"> </span>&gt;<span class="w"> </span>eq1.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Soft equilibration to improve side chain solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd2<span class="w"> </span>+p8<span class="w"> </span>eq2.conf<span class="w"> </span>&gt;<span class="w"> </span>eq2.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
Expand Down Expand Up @@ -490,6 +494,10 @@ <h4>1.5.2 NAMD3<a class="headerlink" href="#namd3" title="Link to this heading">
<p class="admonition-title">Note</p>
<p>In this stage, the restriction file <code class="docutils literal notranslate"><span class="pre">prot_restraints.pdb</span></code> is assigned to the consref and conskfile flags.</p>
</div>
<p><strong>Solvent equilibration (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd3<span class="w"> </span>+p4<span class="w"> </span>eq1.conf<span class="w"> </span>&gt;<span class="w"> </span>eq1.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
</div>
<p><strong>Soft equilibration to improve side chain solvation (NPT):</strong></p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>namd3<span class="w"> </span>+p4<span class="w"> </span>eq2.conf<span class="w"> </span>&gt;<span class="w"> </span>eq2.log<span class="w"> </span><span class="p">&amp;</span>
</pre></div>
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2 changes: 2 additions & 0 deletions _sources/Developers.rst.txt
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Expand Up @@ -12,6 +12,8 @@ Developers

* Andres Ballesteros

* Antonella Alba

* Ezequiel N. Frigini

* Matias Machado
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15 changes: 14 additions & 1 deletion _sources/NAMD/Tutorial-1.rst.txt
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Expand Up @@ -3,7 +3,7 @@
Please report bugs, errors or enhancement requests through `Issue Tracker <https://github.com/SIRAHFF/documentation/issues>`_ or if you have a question about SIRAH open a `New Discussion <https://github.com/SIRAHFF/documentation/discussions>`_.

This tutorial shows how to use the SIRAH force field to perform a coarse grained (CG) simulation of a protein in explicit solvent (called WatFour, WT4). The main references for
this tutorial are: `Darré et al. <https://pubs.acs.org/doi/abs/10.1021/ct100379f>`_, `Machado et al. <https://doi.org/10.1021/acs.jctc.9b00006>`__ and `Machado & Pantano <https://academic.oup.com/bioinformatics/article/32/10/1568/1743152>`_. We strongly advise you to read these articles before starting the tutorial.
this tutorial are: `Cantero et al. <https://doi.org/10.1021/acs.jpcb.4c03278>`_, `Darré et al. <https://pubs.acs.org/doi/abs/10.1021/ct100379f>`_, `Machado et al. <https://doi.org/10.1021/acs.jctc.9b00006>`__ and `Machado & Pantano <https://academic.oup.com/bioinformatics/article/32/10/1568/1743152>`_. We strongly advise you to read these articles before starting the tutorial.

.. important::

Expand Down Expand Up @@ -274,6 +274,12 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD2`` contains typical input files fo

In this stage, the restriction file ``prot_restraints.pdb`` is assigned to the consref and conskfile flags.

**Solvent equilibration (NPT):**

.. code-block:: bash
namd2 +p8 eq1.conf > eq1.log &
**Soft equilibration to improve side chain solvation (NPT):**

.. code-block:: bash
Expand Down Expand Up @@ -372,6 +378,13 @@ The folder ``sirah.amber/tutorial/NAMD/1/NAMD3`` contains typical input files fo

In this stage, the restriction file ``prot_restraints.pdb`` is assigned to the consref and conskfile flags.

**Solvent equilibration (NPT):**

.. code-block:: bash
namd3 +p4 eq1.conf > eq1.log &
**Soft equilibration to improve side chain solvation (NPT):**

.. code-block:: bash
Expand Down
2 changes: 1 addition & 1 deletion searchindex.js
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