mol_model_course_2022

Workshop: Using PLUMED to enhance sampling in Gromacs

Description

• We will outline basic methods of working with PLUMED.
• Duration: 90 minutes
• Objectives: be able to
  • Setup simulations using PLUEMD+GROMACS
  • Define collective variables
  • Setup various types of biased simulations
  • Perform steered MD
  • Perform Metadynamics simulations

Jupyter notebooks

• We follow this tutorial but use updated files.
• plumed_intro.ipynb
• plumed_bias.ipynb
• plumed_metad_intro.ipynb

Required software and resources

• Access to a Jupyter notebook evironment with Python 3, MDanalysis, nglview libraries
• Access to Newton cluster with Gromacs+PLUMED installed or install Gromacs and PLUMED at your local workstation. See http://www.gromacs.org http://www.plumed.org
• We will use mol_model_course_PLUMED conda environment on newton.

Learning resources

• A quick introduction to PLUMED
• Video lecture on MetaDynamics
• PLUMED manual

Assignments

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.

Troubleshooting

• Consult with the seminar protocol/recording
• Ask questions in Slack