Update ASE-OpenMM tutorial notebooks (#255)

* Refactor notebook names of ASE examples * Switch from old runner to OmniRunner and ASEOpenMMSimulation * Refactor simulation name and set up interactive buttons to work with OmniRunner and ASEOpenMMSimulation objects * Add OmniRunner and ASEOpenMMSimulation functionality to nanotube notebook * Make notebook print temperature correctly * Correct path to retrieve port * Remove lines pertaining to old runner * Initial changes to neuraminidase notebook for ASE * Fix temperature units and add ASE-type functionality back into notebook * Undo incorrect changes from merge * Update simulation and runner information * Correct typo * Add ASE functionality back into the nanotube notebook * Add note about ASE units * Rerun notebook to update values * Remove unnecessary semicolons and rerun notebook * Update wording of nanotube notebooks to reflect NanoVer NGLView client * Edit introductory paragraph of notebook
IRL2 · Oct 11, 2024 · 7e855f8 · 7e855f8
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diff --git a/examples/ase/basic_example.ipynb → examples/ase/ase_basic_example.ipynb b/examples/ase/basic_example.ipynb → examples/ase/ase_basic_example.ipynb
@@ -1641,7 +1641,7 @@
     "\n",
     "This notebook showed a toy example with ASE. \n",
     "\n",
-    "* Run bigger molecular mechanics simulations with OpenMM. The [nanotube](./openmm_nanotube.ipynb) and [neuraminidase](./openmm_neuraminidase.ipynb) examples show how to set up simulations with OpenMM.\n",
+    "* Run bigger molecular mechanics simulations with OpenMM. The [nanotube](./ase_openmm_nanotube.ipynb) and [neuraminidase](./ase_openmm_neuraminidase.ipynb) examples show how to set up simulations with OpenMM.\n",
     "* To understand what's going on under the hood, consider starting with the [NanoVer frame explained](../fundamentals/frame.ipynb) example. "
    ]
   },