Update default settings

Author: hannahbaumann

openmm_septop/python_tutorial.ipynb

@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "id": "fc97de03",
    "metadata": {},
    "outputs": [],
@@ -84,7 +84,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "Generating charges: 100%|███████████████████████| 10/10 [02:35<00:00, 15.56s/it]\n"
+      "Generating charges: 100%|███████████████████████| 10/10 [02:41<00:00, 16.12s/it]\n"
      ]
     }
    ],
@@ -125,7 +125,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 4,
    "id": "5a3cf244",
    "metadata": {},
    "outputs": [],
@@ -145,7 +145,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 5,
    "id": "f6e7bce5",
    "metadata": {},
    "outputs": [],
@@ -167,7 +167,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 6,
    "id": "e6ca6131",
    "metadata": {},
    "outputs": [
@@ -178,7 +178,7 @@
        "<Figure size 800x800 with 1 Axes>"
       ]
      },
-     "execution_count": 26,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -198,7 +198,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 7,
    "id": "2263838f",
    "metadata": {},
    "outputs": [],
@@ -320,18 +320,36 @@
    "id": "56658a3a",
    "metadata": {},
    "source": [
-    "We'll use the default settings for the `Protocol` in this tutorial."
+    "There are various different parameters which can be set to determine how the SepTop simulation will take place.\n",
+    "\n",
+    "The easiest way to customize protocol settings is to start with the default settings, and modify them. Many settings carry units with them.\n",
+    "\n",
+    "Here, we will change the default simulation time to speed things up for the tutorial."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 14,
+   "id": "c2b3de6d-1f11-432d-82f3-9deff16c78dc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from openff.units import unit\n",
+    "settings = SepTopProtocol.default_settings()\n",
+    "settings.solvent_simulation_settings.equilibration_length = 10 * unit.picosecond\n",
+    "settings.solvent_simulation_settings.production_length = 500 * unit.picosecond\n",
+    "settings.complex_simulation_settings.equilibration_length = 10 * unit.picosecond\n",
+    "settings.complex_simulation_settings.production_length = 500 * unit.picosecond"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
    "id": "7adf42d6",
    "metadata": {},
    "outputs": [],
    "source": [
-    "default_settings = SepTopProtocol.default_settings()\n",
-    "protocol = SepTopProtocol(default_settings)"
+    "protocol = SepTopProtocol(settings)"
    ]
   },
   {
@@ -346,7 +364,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "id": "44ba94ca",
    "metadata": {},
    "outputs": [],
@@ -383,7 +401,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 17,
    "id": "66666a80",
    "metadata": {},
    "outputs": [],
@@ -428,7 +446,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 18,
    "id": "d6cebd9a",
    "metadata": {},
    "outputs": [],
@@ -445,7 +463,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 19,
    "id": "b96b57a9",
    "metadata": {},
    "outputs": [
@@ -499,7 +517,7 @@
    "metadata": {},
    "source": [
     "Finally now that we've run our simulations, let's go ahead and gather the free energies for both phases.\n",
-    "If you ran the simulation using the CLI (i.e. by calling openfe quickrun ) you will end up with a JSON output file fpr each transformation. To get your simulation results you can load them back into Python in the following manner:"
+    "If you ran the simulation using the CLI (i.e. by calling openfe quickrun ) you will end up with a JSON output file for each transformation. To get your simulation results you can load them back into Python in the following manner:"
    ]
   },
   {