Restructure fundamentals directory (#237)

* Add basics directory to examples and move getting_started.ipynb and nanover_nglview.ipynb to this directory

* Remove nglclient.py from LAMMPS directory and change lammps tutorial to use nanover.nglview module instead

* Change path to NGLView notebook example

* Copy nanotube.xml imput file to local openmm_files directory and change path in getting_started.ipynb

examples/ase/basic_example.ipynb

@@ -360,9 +360,7 @@
   {
    "cell_type": "markdown",
    "metadata": {},
-   "source": [
-    "You can also visualize it live in the notebook, (check out this [example with NGLView](nanover_nglview.ipynb))."
-   ]
+   "source": "You can also visualize it live in the notebook, (check out this [example with NGLView](../basics/nanover_nglview.ipynb))."
   },
   {
    "cell_type": "markdown",

examples/ase/openmm_nanotube.ipynb

@@ -606,7 +606,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "* The [NGLViewer notebook](nanover_nglview.ipynb) is a smaller notebook designed for visualizing your own simulations.\n",
+    "* The [NGLViewer notebook](../basics/nanover_nglview.ipynb) is a smaller notebook designed for visualizing your own simulations.\n",
     "* Set up an OpenMM simulation with an AMBER file for a [protein-ligand system](openmm_neuraminidase.ipynb) and simulate it in NanoVer\n",
     "* Set up a simulation of a [graphene sheet](openmm_graphene.ipynb) with parameters than can be controlled from the jupyter notebook. \n",
     "* Visualize an [LSD receptor in a membrane](../mdanalysis/mdanalysis_lsd.ipynb) structure with MDAnalysis and NanoVer "

examples/fundamentals/getting_started.ipynb → examples/basics/getting_started.ipynb

@@ -126,7 +126,7 @@
    },
    "outputs": [],
    "source": [
-    "input_xml = \"../openmm/openmm_files/nanotube.xml\"\n",
+    "input_xml = \"openmm_files/nanotube.xml\"\n",
     "nanotube_simulation = OpenMMSimulation.from_xml_path(input_xml)"
    ]
   },