[WIP] Wizard and compile

wizard_and_compile/README.md

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+This mini-tutorial deals with two tools for setting up simulations using the
+OpenPathSampling CLI: the Wizard and the `compile` command.
+
+
+## Requirements
+
+This tutorial requires OpenPathSampling, the OpenPathSampling CLI, OpenMM, and
+OpenMMTools.
+
+## Alanine dipeptide
+
+The system we will study is alanine dipeptide. It's a boring, simple system,
+but one that you can easily run on a laptop, and one that illustrates the
+basics of path sampling very well.
+
+In this mini-tutorial, we provide the necessary (solvated and equilibrated)
+inputs to run TPS. To learn how to set up an OpenMM simulation, we recommend
+the [OpenMM documentation](http://docs.openmm.org). To learn how to get an
+initial trajectory for path sampling simulations, we have several other
+tutorials, such as the `simstore_and_cli` tutorial in this repository. Simple
+scripts to generate the necessary files (requiring OpenMMTools) are provided in
+the `prereqs` directory.
+
+
+## Target TPS setup
+
+* **Engine**: The engine should use the provided PDB for topology, and the
+  provided integrator and system XML files. That integrator uses a 2 fs
+  timestep; you should save frames every 20 fs, and abort any trajectory that
+  runs for 20 ps. (Note: timescales for practical biomolecular systems are
+  usually much longer, saving frames on the order of every picosecond and
+  allowing trajectories of 10s or even 100s of nanoseconds.)
+* **CVs**: The CVs we use here are the phi and psi dihedral angles. The atoms
+  that define them (counting from 0) are:
+
+  * *phi*: 4, 6, 8, 14
+  * *phi*: 6, 8, 14, 16
+
+  To learn how to identify those atom numbers in practice, we recommend the
+  [Python-based tutorial](http://github.com/openpathsampling/ops_tutorial),
+  which shows how to use MDTraj to identify them.
+
+* **States**: We'll look at the transition from the `C_7eq` state to the
+  `alpha_R` state. These states are defined by the following (in degrees):
+
+  * `C_7eq`: -180 <= phi < 0  and 100 <= psi < 200
+  * `alpha_R`: -180 <= phi < 0 and -100 <= psi < 0
+
+  Note that these are in degrees; since MDTraj reports dihedrals in radians,
+  you'll need to scale these numbers by pi/180 to get radians.
+
+* **TPS Details**: When setting up with the Wizard, use uniform shooting point
+  selection. When setting up with the ``compile`` command, an example with
+  uniform shooting point selection is already provided, and you should create a
+  second option with a Gaussian biased shooting point selection based on the
+  `psi` variable, with mean at 50 degrees and standard deviation 10 degrees.
+
+## Using the Wizard
+
+First, we recommend using the OPS Wizard to set up this simulation. The Wizard
+will guide you through every step necessary to set up the simulation. Start the
+Wizard with the command `openpathsampling wizard`.
+
+## Using the `compile` command
+
+For the part of this tutorial with the compile command,