domainswap

The domainswap task performs a targeted (steered) molecular-dynamics simulation that swaps a defined structural domain between chains — for example, exchanging the position of a domain on chain A with the equivalent domain on chain B. A domain, selected by the VMD atomselect string swap_domain_def, is biased toward its partner chain’s location while anchor regions (anchor_domain_def) are held in place, using collective-variable harmonic restraints in NAMD. The pairing of chains to swap is given by chain_directional_swaps (e.g. [[A, B], [B, A]] swaps A and B).

This is an advanced task; the complete parameter list is in domainswap, and the underlying Tcl is the domainswap.tcl script.

tasks:
  - ...
  - domainswap:
      swap_domain_def: "protein and resid 1 to 100"
      anchor_domain_def: "protein and resid 200 to 300"
      chain_directional_swaps: [[A, B], [B, A]]
      force_constant: 200.0
      nsteps: 10000