Bug fixes in MD setup & complex MD setup

bioexcel · Jun 25, 2024 · 5acaa8b · 5acaa8b
1 parent 5a06700
commit 5acaa8b
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/biobb_wf_md_setup/docs/source/tutorial.md b/biobb_wf_md_setup/docs/source/tutorial.md
@@ -365,7 +365,8 @@ from biobb_gromacs.gromacs.genion import genion
 output_genion_gro = pdbCode+'_genion.gro'
 output_genion_top_zip = pdbCode+'_genion_top.zip'
 prop={
-    'neutral':True
+    'neutral':True,
+    'concentration':0
 }
 
 # Create and launch bb

diff --git a/biobb_wf_md_setup/html/biobb_wf_md_setup.web.html b/biobb_wf_md_setup/html/biobb_wf_md_setup.web.html
@@ -8163,6 +8163,7 @@ <h3 id="Step-2:-Adding-ions-to-neutralize-the-system">Step 2: Adding ions to neu
 <span class="n">output_genion_top_zip</span> <span class="o">=</span> <span class="n">pdbCode</span><span class="o">+</span><span class="s1">'_genion_top.zip'</span>
 <span class="n">prop</span><span class="o">=</span><span class="p">{</span>
     <span class="s1">'neutral'</span><span class="p">:</span><span class="kc">True</span>
+    <span class="s1">'concentration'</span><span class="p">:</span><span class="mf">0</span>
 <span class="p">}</span>
 
 <span class="c1"># Create and launch bb</span>

diff --git a/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb b/biobb_wf_md_setup/notebooks/biobb_wf_md_setup.ipynb
@@ -499,7 +499,8 @@
     "output_genion_gro = pdbCode+'_genion.gro'\n",
     "output_genion_top_zip = pdbCode+'_genion_top.zip'\n",
     "prop={\n",
-    "    'neutral':True\n",
+    "    'neutral':True,\n",
+    "    'concentration':0\n",
     "}\n",
     "\n",
     "# Create and launch bb\n",