mol_model_course_2023

Workshop: Analyzing MD simulations in Gromacs

Description

Jupyter notebook

Required software and resources

Learning resources

Assignments

From previous assignments you should have a simulation for a protein of your choice set up in Gromacs. You may need to adjust the simulation parameters if needed (trajectory write parameters, duration, temperature etc). Following analyses of this system will be needed as an assignment:

Seminar 6

  1. Plot RMSD matrix for MD frames; perform cluster analysis for mainchain+H atoms; visualize clusters and dynamics of systems transitions between them
  2. Perform PCA: plot atom covariance matrix, eigenvalues plot, calculate fraction of explained variability by first 6 vectors, make vector implementations and make representing first eigenvectors snapshots.

Troubleshooting