clarifications after UvA BioMolSim 2018 tutorial

Author: dwhswenson

1_tps_sampling_tutorial.ipynb

@@ -308,13 +308,20 @@
     "initial_conditions = scheme.initial_conditions_from_trajectories(init_traj)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This should tell you that there are no missing ensembles and no extra ensembles. If not, then there's a problem with your definition of the $\\alpha_R$ state or with your definition of the $\\psi$ collective variable. Check those very carefully."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Running the simulation\n",
     "\n",
-    "Now all the parts in place, and we can run the simulation! First, we open a file to store the results in, and then we build the simulation and run it."
+    "Now all the parts are in place, and we can run the simulation! First, we open a file to store the results in, and then we build the simulation and run it."
    ]
   },
   {
@@ -346,6 +353,13 @@
    "source": [
     "storage.close()"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You're done running the (short) simulation. In the next notebook, we'll analyze these results, and then do a more thorough analysis of a longer simulation."
+   ]
   }
  ],
  "metadata": {

2_tps_analysis_tutorial.ipynb

@@ -129,7 +129,8 @@
    "outputs": [],
    "source": [
     "# YOUR TURN: load a trajectory from your simulation. \n",
-    "# Replace #### in the next line (and uncomment it).\n",
+    "# Replace #### in the line below with the number of one of your steps\n",
+    "# (and uncomment it the line).\n",
     "#traj = storage.steps[####].active[0].trajectory"
    ]
   },
@@ -454,7 +455,7 @@
    },
    "outputs": [],
    "source": [
-    "# YOUR TURN: find those trajectories. Find the right numbers to replace #### below (and uncomment them).\n",
+    "# YOUR TURN: find such trajectories. Find the right numbers to replace #### below (and uncomment them).\n",
     "# The next cell will plot the trajectories.\n",
     "# trajA = flexible.steps[####].active[0].trajectory\n",
     "# trajB = flexible.steps[####].active[0].trajectory"