Exercise 1: Fix charge calculation distance

Author: amruthesht

workshop/solutions.ipynb

@@ -17,7 +17,7 @@
     "\n",
     "## Exercise 1 Solution: Charge Density Analysis\n",
     "\n",
-    "Calculate the total charge within 4 Å of the protein at each timestep."
+    "Calculate the total charge within 8 Å of the protein at each timestep."
    ]
   },
   {
@@ -26,31 +26,30 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
     "import numpy as np\n",
     "from graph_utils import live_plot\n",
     "\n",
     "u = mda.Universe(\"sample_simulation/GROMACS/input/start.gro\", \"imd://localhost:8889\", buffer_size=100*1024**2)\n",
     "\n",
     "try:\n",
-    "    # Select solvent atoms within 4 Å of protein (updating each frame)\n",
-    "    nearby = u.select_atoms('not protein and around 4 protein', updating=True)\n",
+    "    # Select Na+ and Cl- ions within 8 Å of protein (updating each frame)\n",
+    "    na_sel = u.select_atoms('resname SOD and around 8 protein', updating=True)\n",
+    "    cl_sel = u.select_atoms('resname CLA and around 8 protein', updating=True)\n",
     "\n",
     "    # Create live plot\n",
     "    plot = live_plot(\n",
-    "        title=\"Charge Density within 4 Å\",\n",
+    "        title=\"Net Ion Charge within 8 Å\",\n",
     "        ylabel=\"Total Charge (e)\",\n",
     "        update_interval=1\n",
     "    )\n",
     "\n",
     "    for ts in u.trajectory:\n",
-    "        # Calculate total charge in selection\n",
-    "        total_charge = np.sum(nearby.charges)\n",
+    "        n_na = na_sel.n_atoms\n",
+    "        n_cl = cl_sel.n_atoms\n",
+    "        total_charge = n_na - n_cl  # +1 for Na, -1 for Cl\n",
     "        plot['update'](ts.time, total_charge)\n",
-    "        \n",
-    "        \n",
-    "        print(f\"Frame {ts.frame:4d} | Time: {ts.time:8.2f} ps | Charge: {total_charge:+.4f} e | Atoms: {nearby.n_atoms}\")\n",
+    "        print(f\"Frame {ts.frame:4d} | Time: {ts.time:8.2f} ps | Na+: {n_na} | Cl-: {n_cl} | Net Charge: {total_charge:+d} e\")\n",
     "\n",
     "except Exception as e:\n",
     "    print(f\"\\n\\nError: {e}\")\n",
@@ -80,13 +79,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from imdclient.IMD import IMDReader\n",
     "import MDAnalysis as mda\n",
     "from MDAnalysis.analysis import rms\n",
     "import numpy as np\n",
     "from graph_utils import live_plot\n",
     "\n",
     "u = mda.Universe(\"sample_simulation/GROMACS/input/start.gro\", \"imd://localhost:8889\", buffer_size=100*1024**2)\n",
+    "# Have fixed axis for better visualization\n",
+    "# plot[\"ax\"].set_xlim(0, 100)  # Time axis from 0 to 100 ps\n",
+    "# plot[\"ax\"].set_ylim(13, 16)   # Rg axis from 13 to 16 Å\n",
     "\n",
     "try:\n",
     "    # Select backbone atoms (N, CA, C, O - the protein main chain)\n",
@@ -127,13 +128,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "workshop",
    "language": "python",
    "name": "python3"
   },
   "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
    "name": "python",
-   "version": "3.10.0"
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.14.0"
   }
  },
  "nbformat": 4,

workshop/workshop.ipynb

@@ -468,7 +468,7 @@
     "\n",
     "## 🎯 Exercise 1: Charge Density Analysis\n",
     "\n",
-    "**Your Task**: Calculate the **total charge within 4 Å of the protein** at each timestep.\n",
+    "**Your Task**: Calculate the **total charge within 8 Å of the protein** at each timestep.\n",
     "\n",
     "This is an important property for understanding:\n",
     "- Electrostatic environment around the protein\n",
@@ -482,7 +482,7 @@
     "solvent = u.select_atoms('not protein')\n",
     "```\n",
     "\n",
-    "**Distance-based selection** (solvent within 4 Å of protein):\n",
+    "**Distance-based selection** (solvent within 8 Å of protein):\n",
     "```python\n",
     "# Use updating=True to recalculate selection each frame!\n",
     "nearby = u.select_atoms('not protein and around 4 protein', updating=True)\n",
@@ -525,10 +525,10 @@
     "    ## Your code here!\n",
     "    ## \n",
     "    ## Steps:\n",
-    "    ## 1. Create selection for nearby solvent: nearby = u.select_atoms('not protein and around 4 protein', updating=True)\n",
-    "    ## 2. Create live plot: plot = live_plot(\"Charge Density within 4 Å\", ylabel=\"Total Charge (e)\")\n",
+    "    ## 1. Create selection for nearby ions: na_sel = u.select_atoms('resname SOD and around 8 protein', updating=True) and similary for 'CLA' ions\n",
+    "    ## 2. Create live plot: plot = live_plot(\"Charge Density within 8 Å\", ylabel=\"Total Charge (e)\")\n",
     "    ## 3. Loop through frames\n",
-    "    ## 4. Calculate total_charge = np.sum(nearby.charges)\n",
+    "    ## 4. Calculate total_charge = na_sel - cl_sel\n",
     "    ## 5. Update plot: plot['update'](ts.time, total_charge)\n",
     "    \n",
     "    pass  # Remove this and add your code\n",