iSoLF

iSoLFAttractivePotential #

iSoLFAttractive attractive part of the iSoLF potential for coarse-grained lipids developed by the following paper.

\[U(r) = \begin{cases} -\epsilon_{ij} & r_{ij} < \sqrt[6]{2}\sigma_{ij}\\ -\epsilon_{ij} \cos^2\left[\frac{\pi}{2\omega_{ij}}(r_{ij} - \sqrt[6]{2}\sigma_{ij}) \right] & (\sqrt[6]{2}\sigma_{ij} < r_{ij} < \sqrt[6]{2}\sigma_{ij} + \omega_{ij})\\ 0 & (\sqrt[6]{2}\sigma_{ij} + \omega_{ij} < r_{ij}) \end{cases}\]

Example #

[[forcefields.global]]
interaction = "Pair"
potential   = "iSoLFAttractive"
ignore.particles_within = {bond = 1, angle = 1}
ignore.group.inter = [
    ["T1", "T3"]
]
spatial_partition = {type = "CellList", margin = 0.5}
env.popc_epsilon = 0.416
env.popc_omega   = 9.867
env.popc_sigma_T = 7.111
parameters = [
{index =     2, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
{index =     3, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
{index =     4, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
{index =     7, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
{index =     8, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
{index =     9, sigma = "popc_sigma_T", epsilon = "popc_epsilon", omega = "popc_omega"},
# ...
]

Input Reference #

To calculate \( \sigma \) , \( \epsilon \) and \( \omega \) for each pair, Lorentz-Berthelot combining rules are used.

\[\sigma_{ij} = \frac{\sigma_i + \sigma_j}{2} \\ \epsilon_{ij} = \sqrt{\epsilon_i\epsilon_j} \\ \omega_{ij} = \frac{\omega_i\omega_j}{2}\]
  • index: Integer
    • The index of the particle.
  • offset: Integer (optional. By default, 0.)
    • Offset value of the index.
  • sigma: Floating
    • It determines the effective particle size.
  • epsilon: Floating
    • It determines the strength of the potential.
  • omega: Floating
    • It determines the width of the attractive well.

Since this potential becomes exactly 0 at \( r = \sqrt[6]{2}\sigma_{ij} + \omega_{ij} \) , always this cutoff distance is used. You don’t need to set cutoff.

For other values, see Pair.