mol_model_course

Workshop: Introduction to MD simulations

Description

Jupyter notebook

Learning resources

Assignments

Perform energy minimization of a protein in Gromacs.

  1. Plot energy versus step.
  2. Compare steepest descent, conjugate gradient and L-BFGS methods.

Suggested problem sets

Each student should take a unique PDB structure at his/her own discretion.

Troubleshooting