diff --git a/examples/ase/ase_openmm_nanotube.ipynb b/examples/ase/ase_openmm_nanotube.ipynb index 118f61ff..e1798118 100644 --- a/examples/ase/ase_openmm_nanotube.ipynb +++ b/examples/ase/ase_openmm_nanotube.ipynb @@ -198,7 +198,9 @@ { "cell_type": "markdown", "metadata": {}, - "source": "As we are running the OpenMM simulation via ASE, we can use the ASE functionality to run a few simulation steps to check that everything is working:" + "source": [ + "As we are running the OpenMM simulation via ASE, we can use the ASE functionality to run a few simulation steps to check that everything is working:" + ] }, { "cell_type": "code", @@ -248,7 +250,7 @@ { "data": { "text/plain": [ - "29.37619863848655" + "0.30069013433609304" ] }, "execution_count": 7, @@ -257,6 +259,7 @@ } ], "source": [ + "# Note that this is the energy in eV, not kJ mol-1 (the standard units of ASE are different to those of OpenMM and NanoVer)\n", "nanotube_simulation.dynamics.atoms.get_potential_energy()" ] }, @@ -324,7 +327,7 @@ { "data": { "text/plain": [ - "24.45851002327552" + "5.304255185770594" ] }, "execution_count": 9, @@ -390,7 +393,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "2039748b2f864b1f94024a907af8b5c1", + "model_id": "e73ec3466e28447fbacfb2117035b005", "version_major": 2, "version_minor": 0 },