README.md

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. 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, 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,