typo fix

MD_in_Colab(ENG).ipynb

@@ -15,7 +15,7 @@
         "B8BgKwrGEKsT"
       ],
       "gpuType": "T4",
-      "authorship_tag": "ABX9TyOSScmfzqpwnZ7YjaT+cDKt",
+      "authorship_tag": "ABX9TyMXHRsLdBrkj+79swqWHnbe",
       "include_colab_link": true
     },
     "kernelspec": {
@@ -20693,7 +20693,7 @@
         "\n",
         "print(\"Check whether the system's apparent temperature stabilizes to the desired value.\")\n",
         "print(\"Check also the system's density stabilizes to a value near 1.04 g/mL for physiological conditions.\")\n",
-        "print(\"If not, go back to the cell 3. Set MD parameters and increase the eq_time.\")\n",
+        "print(\"If not, go back to the cell# 3-2.\")\n",
         "print(\"If yes, proceed to the next cell.\")"
       ],
       "metadata": {
@@ -20914,9 +20914,9 @@
         "#@title 4-1. Wrap and View Trajectory\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
         "\n",
-        "#@markdown This cell will concatenate the trajectories generated during the Step 4-1, 4-2, and 4-3. <br/>\n",
+        "#@markdown This cell will concatenate the trajectories generated during the Step 3-1, 3-2, and 3-3. <br/>\n",
         "#@markdown Check the box below to produce a 'smoothed' final trajectory. <br/>\n",
-        "#@markdown Download your trajectories whose names end with either _final.xtc or _smoothed.xtc from your GoogleDrive!\n",
+        "#@markdown Download your trajectories whose names end with _final.xtc from your GoogleDrive!\n",
         "\n",
         "smooth_trajectory = False #@param {type:\"boolean\"}\n",
         "\n",
@@ -21460,6 +21460,8 @@
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
         "assert os.path.exists(work+'production.h5'), \"Run the cell# 4-1 first to wrap the trajectory.\"\n",
         "\n",
+        "#@markdown Shows the free energy landscape calculated from the kernel density of given macrostate.\n",
+        "\n",
         "traj = md.load(work+'production.h5')\n",
         "\n",
         "rmsd = md.rmsd(traj, traj, 0)\n",
@@ -22396,7 +22398,7 @@
     {
       "cell_type": "code",
       "source": [
-        "#@title 5-0. Install dependencies for Binding Free Energy Analysis\n",
+        "#@title 5-1. Install dependencies for Binding Free Energy Analysis\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
         "assert os.path.exists(work+'starting_structure.pdb'), \"starting_structure.pdb file not found!\"\n",
         "assert os.path.exists(work+'production.h5'), \"Result trajectory not found! Run cell# 4-1 first.\"\n",
@@ -22565,7 +22567,7 @@
     {
       "cell_type": "code",
       "source": [
-        "#@title 5-1. Prepare trajectories for MM/GBSA\n",
+        "#@title 5-2. Prepare trajectories for MM/GBSA\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
         "#@markdown Enter the chain ID(s) of ligand and receptor. Separate multiple chains with commas. <br/>\n",
         "#@markdown You can enter only ligand chain ID to make every other chain as receptor.\n",
@@ -22647,9 +22649,9 @@
     {
       "cell_type": "code",
       "source": [
-        "#@title 5-2. Running MM/GBSA\n",
+        "#@title 5-3. Running MM/GBSA\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
-        "assert 'ff' in globals(), \"Please run the cell# 5-1 first.\"\n",
+        "assert 'ff' in globals(), \"Please run the cell# 5-2 first.\"\n",
         "\n",
         "#@markdown Select a Generalized Born model to use.\n",
         "GB_model = \"GBn2 (igb=8)\" #@param [\"HCT (igb=1)\", \"OBC1 (igb=2)\", \"OBC2 (igb=5)\", \"GBn (igb=7)\", \"GBn2 (igb=8)\"]\n",
@@ -23077,9 +23079,9 @@
     {
       "cell_type": "code",
       "source": [
-        "#@title 5-3. Calculate Binding Free Energy from Interaction Entropy & C2 Entropy\n",
+        "#@title 5-4. Calculate Binding Free Energy from Interaction Entropy & C2 Entropy\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
-        "assert 'couls' in globals(), \"Please run the cell# 5-1 first.\"\n",
+        "assert 'couls' in globals(), \"Please run the cell# 5-2 first.\"\n",
         "\n",
         "#@markdown Set the bootstrap sampling size to 10^n.\n",
         "bootstrap_power = 4 #@param {type:\"slider\", min:3, max:8, step:1}\n",
@@ -23277,11 +23279,11 @@
     {
       "cell_type": "code",
       "source": [
-        "#@title 5-4. (Optional) Calculate Binding Entropy via Quasi-harmonic Approximation\n",
+        "#@title 5-5. (Optional) Calculate Binding Entropy via Quasi-harmonic Approximation\n",
         "#@markdown **WARNING: QH method takes very long time for large systems!!**\n",
         "\n",
         "assert 'work' in globals(), \"Please run the cell# 0 to set working directory.\"\n",
-        "assert 'temperature' in globals(), \"Please run the cell# 5-1 first.\"\n",
+        "assert 'temperature' in globals(), \"Please run the cell# 5-2 first.\"\n",
         "\n",
         "#@markdown Set the reference concentration in mol/L for a standard solution of ligand.\n",
         "reference_concentration = 1 #@param {type:\"string\"}\n",