Use positional restraints#

You will learn: how to add positional restraints to an ACEMD simulation, including ramped (time-varying) and flat-bottom variants.

Prerequisites:

See External forces for the full reference of every option used below.

Setup#

Restraints go under the top-level extforces key of your input.yaml file. Each entry has a type and type-specific options. Today the only available type is positionalRestraint:

input.yaml#
extforces:
  - type: positionalRestraint
    sel: "protein and name CA"
    setpoints:
      - 1@0

This applies a 1 kcal/mol/Ų harmonic restraint to every protein Cα for the whole simulation.

Ramp a restraint down during equilibration#

Restraints are usually held strong at the start and released over the equilibration. Use multiple setpoints — values are linearly interpolated between consecutive entries:

input.yaml#
extforces:
  - type: positionalRestraint
    sel: "protein and name CA"
    setpoints:
      - 1@0ns
      - 0@10ns

Time suffixes (fs, ps, ns, us) or raw step counts are both accepted. A bare number means steps, not nanoseconds — 0@2500000 is “at step 2,500,000”, whereas 0@2500000ns is “at 2.5 ms of simulated time”. Prefer the suffixed form to avoid ambiguity.

Restrain inside a flat-bottom box around a moving centre#

fbCenter with an atom selection makes the restraint follow the centre of mass of that selection. Pair it with fbWidth to define a tolerance box:

input.yaml#
extforces:
  - type: positionalRestraint
    sel: "resname MOL"
    fbwidth: 10
    fbcenter: "protein and name CA"
    setpoints:
      - 0.5@0

The ligand is free to move within a 10 Å box centred on the protein’s Cα COM, and pushed back if it leaves.

Restrain inside a slab above the membrane#

A common pattern for membrane-permeation simulations — keep ligands inside a 20 Å slab centred 10 Å above the bilayer:

input.yaml#
extforces:
  - type: positionalRestraint
    sel: "resname MOL and noh"
    axes: "z"
    fbwidth: 20
    fbcenter: "(lipid or resname AR CHL DHA LAL MY OL PA PC PE PGR PGS PS SA SPM ST) and noh"
    fbcenteroffset: [0, 0, 10]
    setpoints:
      - 0.5@0

The lipid selection above is the authoritative residue list used by ACEMD’s cellular-restraint helper — it is defined once as the constant LIPIDSEL in acemd.protocols. If you build your own membrane selection, keep it in sync with that source of truth.

For the symmetric case (above and below the membrane), get_cellular_restraints() builds the YAML for you.

Restrain only one direction#

A + or - prefix on an axis activates the restraint only when the atom moves in that direction from its reference position; motion in the opposite direction is unrestrained. With axes: "+z" the atom is pulled back if it tries to move in +z, but is free to move in -z:

input.yaml#
extforces:
  - type: positionalRestraint
    sel: "resname LIG"
    axes: "+z"
    setpoints:
      - 1@0

Here the ligand can sink to lower z (e.g. through a membrane) but is held back from rising above its starting z. Flip to axes: "-z" for the opposite: free upward motion, blocked downward.

Use a reference PDB instead of the starting coordinates#

The top-level option fbRefCoor reads reference atom positions from a separate PDB. Useful when you want the restraints to pull back toward, say, a crystal pose rather than the equilibrated starting frame:

input.yaml#
fbrefcoor: crystal.pdb
extforces:
  - type: positionalRestraint
    sel: "protein and name CA"
    setpoints:
      - 1@0

The reference PDB must match the simulation system atom-for-atom.

Gotchas#

  • Exclude hydrogens at timestep > 2 fs. Constrained hydrogens combined with strong harmonic restraints can produce NaN coordinates. Use and noh on your selection.

  • Restraint mass is in your selection. If fbCenter is an atom selection and the selection is empty, ACEMD raises during setup. Verify the selection picks atoms.

See also#