Not only querying, but also modifying system parameters

notebooks/cookbook/Querying Charges and Other Parameters.ipynb → notebooks/cookbook/Querying and Modifying Charges and Other Parameters.ipynb

@@ -5,14 +5,14 @@
    "id": "3a4fdeed",
    "metadata": {},
    "source": [
-    "## Querying Charges and Other Parameters\n",
+    "## Querying and Modifying Charges and Other Parameters\n",
     "\n",
     "Sometimes you want to inspect the charges or other parameters of the particles or bonds in a System.  Force field parameters are stored in the Force objects added to a System.  As an example, let's load a PDB file and model it using the Amber14 force field."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "9323aaae",
    "metadata": {},
    "outputs": [],
@@ -35,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "1734190f",
    "metadata": {},
    "outputs": [],
@@ -53,7 +53,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "bf38fc9a",
    "metadata": {},
    "outputs": [],
@@ -76,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "id": "933928f9",
    "metadata": {},
    "outputs": [
@@ -98,12 +98,84 @@
     "    if particle1 == 0 or particle2 == 0:\n",
     "        print(f'Particles ({particle1}, {particle2}), length = {length}, k = {k}')"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "50f5157c",
+   "metadata": {},
+   "source": [
+    "In some cases you may want to modify those parameters to make a bond behave differently from what the `ForceField` assigned.\n",
+    "We show you here that to modify these parameters are also easy."
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "cd5396c5",
+   "metadata": {},
+   "source": [
+    "Let's say we would want to modify the force constant of the bond connecting particle 1 and 0 to a new number."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "086c7629",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for i in range(bonded.getNumBonds()):\n",
+    "    particle1, particle2, length, k = bonded.getBondParameters(i)\n",
+    "    if particle1 == 1 and particle2 == 0:\n",
+    "        bonded.setBondParameters(i, particle1, particle2, length, 2666 * unit.kilojoules_per_mole/unit.nanometer**2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8f9728ad",
+   "metadata": {},
+   "source": [
+    "Now if you query again you can see new parameters."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "68498ff5",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Particles (4, 0), length = 0.1471 nm, k = 307105.5999999999 kJ/(nm**2 mol)\n",
+      "Particles (1, 0), length = 0.101 nm, k = 2666.0 kJ/(nm**2 mol)\n",
+      "Particles (2, 0), length = 0.101 nm, k = 363171.19999999995 kJ/(nm**2 mol)\n",
+      "Particles (3, 0), length = 0.101 nm, k = 363171.19999999995 kJ/(nm**2 mol)\n"
+     ]
+    }
+   ],
+   "source": [
+    "for i in range(bonded.getNumBonds()):\n",
+    "    particle1, particle2, length, k = bonded.getBondParameters(i)\n",
+    "    if particle1 == 0 or particle2 == 0:\n",
+    "        print(f'Particles ({particle1}, {particle2}), length = {length}, k = {k}')"
+   ]
+  },
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "id": "47729e2e",
+   "metadata": {},
+   "source": [
+    "Modifying `Force` objects will affect any new `Simulations` or `Contexts` you create, but it will have no effect on ones that already exist. \n",
+    "If you want your modifications to apply to an existing `Simulation`, you can copy them over by calling `bonded.updateParametersInContext(simulation.context)`."
+   ]
   }
  ],
  "metadata": {
-  "tags": ["force field", "inspection", "forces"],
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -117,8 +189,13 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
-  }
+   "version": "3.11.3"
+  },
+  "tags": [
+   "force field",
+   "inspection",
+   "forces"
+  ]
  },
  "nbformat": 4,
  "nbformat_minor": 5