Analysis of Trajectories Generated from PDB Files [link to iPython viewer]

Omnia Tools:  PDBFixer, OpenMM, MDTraj

This example workflow demonstrates how to run and compare two molecular dynamics trajectories in terms of their RMSD and dihedral angles.  You will use PDBFixer to prepare a molecule from the Protein Data Bank for simulation;  use OpenMM to set up and run an implicit solvent simulation of that molecule using a Langevin integrator; and use MDTraj to compare two simulations that you generate.