Appropriate CVs for WT-METAD to capture docking-undocking study of a nucleic acid

[Sk Habibullah]

Dear plumed users,

        I want to do well-tempered metadynamics simulation to capture docking-undocking study of a nucleic acid. What will be best CVs I can use for this case? Please let me know. I have tried with eRMSD (which can capture the orientation of residues) and distance between two parts of nucleic acid.  But eRMSD considering many residues (15 residues) is a very slow CV. What else CV can I use to consider both orientations and tertiary contacts between different residues? I have thought about contact map CV, but there I need to consider many pairs to capture tertiary contacts between different residues. Will this contact map CV not be very slow for convergence?? 

Thank you in advance,

Habibullah

[Danny Fellner]

This is entirely system-dependent. The only one who can answer these questions is yourself - through experimentation.

Do your CVs capture all (or most) of the relevant degrees of freedom? A CV I don't see in your post is the ligand-binding site distance - this is more important than an internal distance, and should be #1. You should read the relevant papers on Funnel Metadynamics, as a funnel restraint (and longitudinal + radial distance CVs) have proven robust starting points for a variety of systems.

Habibullah4