Author: Dominykas Lukauskis
Email: [email protected]
Requirements:
- BioSimSpace
- OpenMM or Gromacs/Amber patched with PLUMED
This workshop tutorial walks you through how to setup funnel metadynamics (fun-metaD) simulations to estimate the absolute binding free energy (ABFE), how to visualise the funnel restraints and how to analyse the simulations using BioSimSpace.
The workshop is divided into two notebooks.
For a step-by-step guide on how to visualise the funnel restraints and how to set up the fun-metaD simulations, follow this Jupyter NB.
For a step-by-step guide on how to analyse fun-metaD simulations go here. This notebook includes a discussion on how to think about convergence in fun-metaD simulations and how to get a robust ABFE estimate.