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<div class="section" id="xml-settings-file">
<h1>XML settings file<a class="headerlink" href="#xml-settings-file" title="Permalink to this headline">¶</a></h1>
<p>Here we describe structure of XML settings file. Every <strong>dot</strong> describes the tree structure, e.g. <strong>root.a</strong> represents <code class="code xml docutils literal notranslate"><span class="name tag"><span class="pre"><root><a></a></root></span></span></code>.
The notation <em>1</em> or <em>1..N</em> express the number of elements in the tree.</p>
<dl class="docutils">
<dt>settings</dt>
<dd><em>1</em>, root</dd>
<dt>cg_molecule</dt>
<dd><p class="first"><em>1..N</em>, different types of atomistic molecules
defines the list of fragments in given CG molecule.</p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><blockquote class="first">
<div><ul class="simple">
<li>equilibrate_charges: if set to “1” then the partial charges will be adjusted to make the fragment neutral.</li>
</ul>
</div></blockquote>
<dl class="last docutils">
<dt>cg_molecule.name</dt>
<dd>coarse-grained name of the residue</dd>
<dt>cg_molecule.ident</dt>
<dd>name of the residue after backmapping</dd>
</dl>
</dd>
</dl>
</dd>
<dt>cg_molecule.source_coordinate</dt>
<dd><p class="first">name of the coordinate file if there is no need to define it per molecule degree.</p>
<blockquote class="last">
<div><dl class="docutils">
<dt>cg_molecule.source_coordinate.file</dt>
<dd><p class="first">name of the coordinate file that stores atomistic fragment</p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><ul class="first last simple">
<li>molecule_degree: declares that given coordinate file will be used when the molecule is in <em>degree</em></li>
</ul>
</dd>
<dt><strong>remark</strong></dt>
<dd>For every <em>molecule_degree</em> a separate coordinate file can be defined</dd>
</dl>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>cg_molecule.source_topology</dt>
<dd><p class="first">name of the topology file if there is no need to define it per molecule degree.</p>
<blockquote class="last">
<div><dl class="docutils">
<dt>cg_molecule.source_topology.file</dt>
<dd><p class="first">name of topology file (GROMACS format) that stores atomistic fragment</p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><ul class="first last simple">
<li>molecule_degree: declares that given coordinate file will be used when the molecule is in <em>degree</em></li>
</ul>
</dd>
<dt><strong>remark</strong></dt>
<dd>For every <em>molecule_degree</em> a separate topology file can be defined</dd>
</dl>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>cg_molecule.cg_bead</dt>
<dd><p class="first"><em>1..N</em>, definition of coarse-grained beads</p>
<blockquote class="last">
<div><dl class="docutils">
<dt>cg_bead.name</dt>
<dd>the name of CG bead</dd>
<dt>cg_bead.type</dt>
<dd>the type of CG bead</dd>
<dt>cg_bead.beads</dt>
<dd><p class="first">the list of atomistic particles from which the CG bead will be built</p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><ul class="first last simple">
<li>degree: the degree of particular CG bead</li>
<li>molecule_degree: the degree of the whole CG molecule</li>
<li>active_site: the atom that be used to create atomistic bond (format: <cite><chain_name>:<atom_name>:<max_bonds></cite></li>
</ul>
</dd>
<dt><strong>remark</strong></dt>
<dd><em>max_bonds</em> in <em>active_site</em> definition defines the maximum number of bonds that given active site can have.
This take into account existing atomistic bonds. Keep in mind that the package does not know anything about
double bonds. Therefore, if your active site is already connected withing the fragment with other atoms
by double bonds, you should reduce the maximum number of bonds. For instance, if your carbon has already double bond
with other atom, then <em>max_bonds</em> will be 3 instead of 4.</dd>
</dl>
</dd>
<dt>cg_bead.beads.charge_map</dt>
<dd>the list of partial charges that will be assigned to the atoms.
e.g. 0.0 0.0 * * 1.0; by using <a href="#id1"><span class="problematic" id="id2">**</span></a>* user can declare that the partial charge for that atom
will be taken from topology file.</dd>
<dt>cg_bead.beads.remove</dt>
<dd><p class="first">the list of atoms to remove whenever a given active site is used.</p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><ul class="first last simple">
<li>active_site: the name of active site, it should be the same as defined in <em>active_site</em> attribute of <em>cg_beads.beads</em></li>
</ul>
</dd>
</dl>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>cg_configuration</dt>
<dd><em>1</em>, definition of the CG configuration</dd>
<dt>cg_configuration.coordinate</dt>
<dd>the name of input file with the coarse-grained coordinate file</dd>
<dt>cg_configuration.topology</dt>
<dd>the name of input file with the coarse-grained coordinate file</dd>
<dt>hybrid_configuration.file</dt>
<dd>the output hybrid coordinate file</dd>
<dt>hybrid_configuration.format</dt>
<dd>the output of hybrid coordinate file, currently only GROMACS is supported (.gro file)</dd>
<dt>hybrid_topology</dt>
<dd><p class="first"><em>1</em>, the definition of output hybrid topology. The format is similar to the one
used by GROMACS</p>
<blockquote class="last">
<div><dl class="docutils">
<dt>hybrid_topology.file</dt>
<dd>the name of output file</dd>
<dt>hybrid_topology.(bonds|angles|dihedrals)</dt>
<dd><p class="first"><em>1..N</em> defines the atomistic cross-bonds
The content contains a list fo pairs in the format <molecule name>:<atom name></p>
<dl class="last docutils">
<dt><strong>attributes</strong></dt>
<dd><ul class="first last simple">
<li>params: parameters of the bonds</li>
<li>typeid: optional parameter with the numeric label of the bond, useful for converting output topology file to LAMMPS format.</li>
</ul>
</dd>
<dt><strong>remark</strong></dt>
<dd>the parameters in <em>params</em> are directly injected into output topology file. Therefore you can put comments
after <em>;</em> character as in the normal GROMACS topology file.</dd>
</dl>
</dd>
<dt>hybrid_topology.include</dt>
<dd>the include section of hybrid top (do not add #include part) Put every entry in the new line.</dd>
<dt>hybrid_topology.molecule_type</dt>
<dd><p class="first"><em>1</em>, the molecule_type section</p>
<blockquote class="last">
<div><dl class="docutils">
<dt>hybrid_topologoy.molecule_type.name</dt>
<dd>the name of molecule</dd>
<dt>hybrid_topology.molecule_type.exclusion</dt>
<dd>the global exclusion value, based on this the exclusion for non-bonded interactions will be calculated.</dd>
<dt>hybrid_topology.molecule_type.exclusion_cg</dt>
<dd>the exclusion only for CG particles, this value will be used to generate exclusion list only for CG particles</dd>
<dt>hybrid_topology.molecule_type.exclusion_at</dt>
<dd>the exclusion only for atomistic particles, this value will be used to generate exclusion list only for atomistic particles</dd>
</dl>
</div></blockquote>
</dd>
</dl>
</div></blockquote>
</dd>
<dt>hybrid_topology.system</dt>
<dd>the name of system</dd>
</dl>
</div>
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