mm_hse_2023

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 PLUMED+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

• Create NEW conda environment with Python 3.7 and install Gromacs+PLUMED in it using “conda install -c conda-forge -c intbio gromacs=2018.4_plumed_2.5.0” command
• Install MDAnalysis and nglview libraries in this conda environment.

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 MD where the ends of this helix will be stretched with a restraint.
2. Present MD snapshots.
3. Plot of distance between the end C-alpha atoms of the helix with time.

Take the first two amino 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.

(*) 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 be gradually stretched with a moving restraint.
2. Present MD snapshots.
3. Plot of distance between the end C-alpha atoms of the helix with time.

Troubleshooting

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