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Commit e7095d9e authored by Zhefu Li's avatar Zhefu Li
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Update model.html

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...@@ -713,7 +713,7 @@ out=muscure.pdbqt</div> ...@@ -713,7 +713,7 @@ out=muscure.pdbqt</div>
receptor <code>MOR_processed.gro</code> into a single system <code>complex.gro</code>. receptor <code>MOR_processed.gro</code> into a single system <code>complex.gro</code>.
</li> </li>
<pre><code>gmx editconf -f mus_ini.pdb -o mus.gro <pre><code>gmx editconf -f mus_ini.pdb -o mus.gro
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0</code></pre> gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0</code></pre>
<li>Solvate the system in solvent (such as water). From <code>topol.top</code>, it is known that the <li>Solvate the system in solvent (such as water). From <code>topol.top</code>, it is known that the
net charge is 9; add counterions to neutralize the system.</li> net charge is 9; add counterions to neutralize the system.</li>
...@@ -804,8 +804,7 @@ dit xvg_show -f temperature.xvg</code></pre> ...@@ -804,8 +804,7 @@ dit xvg_show -f temperature.xvg</code></pre>
</ul> </ul>
<pre><code>gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr <pre><code>gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr
gmx mdrun -deffnm md_0_10 gmx mdrun -deffnm md_0_10</code></pre>
</code></pre>
<div class="image-container"> <div class="image-container">
<img src="https://static.igem.wiki/teams/5187/wiki-model-fig/mds.png" alt="MDS" <img src="https://static.igem.wiki/teams/5187/wiki-model-fig/mds.png" alt="MDS"
class="shadowed-image" style="width: 100%; max-width: 1000px;"> class="shadowed-image" style="width: 100%; max-width: 1000px;">
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