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jthortonatravitz
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Update simulation_visualisation/simulation_visualisation.ipynb
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
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simulation_visualisation/simulation_visualisation.ipynb

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"id": "75602d58-6709-4d9b-8a52-9896fdc6a0af",
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"metadata": {},
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"source": [
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"## Centring the Ligand with `mdtraj`\n",
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"## Centering the Ligand with `mdtraj`\n",
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"\n",
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"You may have noticed in the view above that the ligand seems to have drifted away from the protein, this is a visualisation artifact caused by the use of periodic boundary conditions and the way in which `OpenMM` tries to ensure that all particle positions are written into a single periodic box. We can fix this, however, using `mdtraj` and the [image_molecules](https://mdtraj.org/1.9.3/api/generated/mdtraj.Trajectory.html?highlight=image_molecules#mdtraj.Trajectory.image_molecules) function:"
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