Workshop: Using PLUMED to enhance sampling in Gromacs
- 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
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.
Take an arbitrary alpha-helix from your protein of interest with length of up to 10 aminoacids:
- Run steered MD where the ends of this helix will we gardually stretched with a moving restrained.
- Present MD stapshots.
- 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).
- Run unbiased simulations of the dipeptide.
- Plot a Ramachandran plot the the phi and psi angles.
- Perform Metadynamics simulations by biasing phi and psi angles.
- Make a comparative Ramachandran plot for the two simulations.
- Consult with the seminar protocol/recording
- Ask questions in Slack