Introduction

sbmOpenMM facilitates the interface between generating Structure Based Models (SBMs) force fields and simulating them with the engine of OpenMM. One of the main advantages of using the library for creating SBMs is the possibility of scripting changes to the force field, parameters and functions. This entails a more powerful way of experimenting with SBM to test if the simplifying assumptions can explain the phenomena of the target protein systems, or, whether modifications can be carried out to explain them more comprehensively.

This set of tutorials have been designed to introduce the use of the sbmOpenMM library for general use.

Basic tutorials

  1. Alpha-Carbon (CA) simulations
  2. All-heavy-Atom (AA) simulations
  3. Estimating folding temperatures
  4. Estimating free energy profiles
  5. Setting up a multi-basin SBM