Workshop: Using PLUMED to enhance sampling in Gromacs


Jupyter notebooks

Required software and resources

Learning resources


Take an arbitrary alpha-helix from your protein of interest with length of up to 10 aminoacids:

  1. Run steered MD where the ends of this helix will we gardually stretched with a moving restrained.
  2. Present MD stapshots.
  3. Plot of distance between the end C-alpha atoms of the helix with time.

Take the first two amio acids from this helix (a dipeptide).

  1. Run unbiased simulations of the dipeptide.
  2. Plot a Ramachandran plot the the phi and psi angles.
  3. Perform Metadynamics simulations by biasing phi and psi angles.
  4. Make a comparative Ramachandran plot for the two simulations.