Native contacts FF

The native contacts force field is described by:

\[ V = \sum \mathsf{LJ}(r, r_0) + \sum \mathsf{Dis}(r, r_0) \]

where the first summation is over the native contacts which are not disulfide bonds, the second summation is over the disulfide bonds and \(r_0\) is the native distance between the residues in contact. \(\mathsf{LJ}\) denotes the standard Lennard-Jones potential:

\[ \mathsf{LJ}(r, r_0) = \varepsilon \left[\left(\frac{r_0}{r}\right)^{12}-2\left(\frac{r_0}{r}\right)^6\right] \]

Note

Note: The depth of the LJ potential is the same for each non-disulfide native contact, and equal to \(1 \varepsilon\). The different types of the contacts (like backbone-backbone or sidechain-sidechain) are also not distinguished.

A special potential can be specified for the native disulfides (i.e. such as appear in the SSBOND pdb file entries, not the derived cysteine pairs or such as may be specified in the sequence file).

Folding/unfolding study

Parameter file entry

# Parameters for the Go-model contacts, as well as some "simulation protocol"
# settings pertaining to these.
native contacts:
  # Whether it's enabled.
  enabled: true

  # Depth of the LJ potential used.
  lj depth: 1 eps

  # Parameters for the native disulfide bonds (the SSBOND entries in
  # the PDB file). NOTE: I'm not sure if it should include all native contacts
  # two cysteines, or only the ones for which an SSBOND record exists.
  disulfide bond force:
    variant: harmonic
    harmonic params:
      H1: 100 eps/A**2
      H2: 0 eps/A**4
      nat_r: 6.0 A
    lj params:
      depth: 4.0 eps
      r_min: 6.0 A

  # Parameters specifying the folding/unfolding study/protocol.
  (un)folding study:
    # Enable early stopping when all contacts are formed or broken (more
    # generally, having changed the state from the native one).
    stop when all are formed/broken: false

    # Measure median first-change (formed -> broken or broken -> formed for
    # unfolding/folding studies respectively) time across multiple trajectories.
    measure median times: false