# Options for pulling with Atomic Force Microscope tips.
AFM simulations:
# Whether to perform such simulations.
perform: false
# Type of the AFM simulation. Options:
# - "stretch": after equilibration, the first and last residues of the first
# chain are pulled apart. To be more specific, the first residue is kept in
# place by a not moving AFM tip of the "const velocity" type, and the last
# one is pulled in the opposite direction by an AFM tip of either "const
# velocity" or "const force" type.
# - "pull, then release": before equilibration, the last residue of the first
# chain is pulled by an AFM tip in a direction from the first to the last
# residue.
type: stretch
# Time window, over which to average the force/velocity of the residues. See
# the discussion above about the precise meaning of the "averaging".
average stats over: 100 tau
# Parameters for the "pull, then release" simulation type.
pull-release params:
# Time over which to pull the
time: 100 tau
# Parameters for the "AFM tips".
tip params:
# Type of the AFM tip used on the last residue of the chain. Options:
# - "const velocity": the AFM tip is attached to the residue with a harmonic
# force, and moves in the prescribed direction.
# - "const force": the "AFM tip" exerts a constant force on the residue,
# so in effect it's not an AFM tip as much as it's just an added force to
# the residue.
type: const velocity
# Parameters for the "const velocity" option.
velocity params:
# Velocity of the AFM tip.
velocity: 5e-3 A/tau
# H1 parameter in the harmonic force V = H1 d^2 + H2 d^4.
H1: 30.0 eps/A**2
# H2 parameter in the harmonic force V = H1 d^2 + H2 d^4.
H2: 0.0 eps/A**2
# Parameters for the "const force" option.
force params:
# Force of the "AFM tip".
force: 1e-2 eps/(A*tau)