OpenMM Intro:
OpenMM is a toolkit for molecular simulation; we will be using the OpenMM Python package to perform Molecular Dynamics (MD) simulations. You will be using OpenMM in Assignment 2 to calculate the energies of a dihedral bond. In this recitation, we will introduce you to the basics of OpenMM and use it to minimize a small peptide and calculate the potential energy before and after minimization. Minimization finds the local minimum on the potential energy surface, which represents an optimized geometry for potential energy.
Recitation Checkoff Instructions
Since we are working with a small system, we will use Google Colab for our analysis (but we will eventually have to use the cluster and its nice GPUs). Access the Colab notebook for this recitation here: OpenMM Recitation
You will be responsible for filling in all cells marked TODO.
Basic (✓): On GradeScope, upload a picture from PyMOL containing the unminimized and minimized peptide including labels or a legend to indicate which is which. You can use a screenshot of a py3Dmol in your notebook or download the structures and visualize them in PyMOL to create fancier graphics. Include the values of the potential energy both before and after minimization.
Extra (✓+): Run a Langevin simulation on the same peptide using a GBN2 implicit solvent model to define the forcefield instead of the ForceField in the linked tutorial. Save a snapshot every 1000 steps as a DCD file and simulation 10k steps. Load the DCD file into PyMOL (first load the system PDB, then the trajectory file) and make a movie of your simulation output (an animated GIF is fine).
Upload your visualizations and reported energies on GradeScope