3SPN2ExcludedVolumePotential #

It is specific to 3SPN2 coarse-grained DNA model.

\[U(r) = \begin{cases} \epsilon \left[\left(\frac{\sigma_{ij}}{r}\right)^{12} - 2\left(\frac{\sigma_{ij}}{r}\right)^6\right] + \epsilon & (r < \sigma_{ij})\\ 0 & (r \geq \sigma_{ij})\\ \end{cases}\]

Example #

[[forcefields.global]]
interaction = "Pair"
potential = "3SPN2ExcludedVolume"
ignore.particles_within.bond       = 1
ignore.particles_within.angle      = 1
ignore.particles_within.dihedral   = 1
ignore.particles_within.nucleotide = 1
spatial_partition = {type = "CellList", margin = 0.4}
parameters = [
    {index =   0, kind = "S"},
    {index =   1, kind = "A"},
    {index =   2, kind = "P"},
    {index =   3, kind = "S"},
]

Input Reference #

index: Integer
- The index of the particle.
offset: Integer (ptional. By default, 0.)
- Offset value of the index.
kind: String
- One of the "S"(sugar), "A", "T", "C", "G"(base), or "P"(phosphate).

For other values, see Pair.