### SPICA Force Field

We describe the molecule using several different interaction functions
in this force field. This is mostly the same as used in the SDK model,
though a torsion potential term is included for cholesterol model. For
intramolecular interaction, we consider harmonic bond stretching and angle
bending potentials for 1-2 and 1-2-3 bonded pairs, while the pairs separated
by more than two bonds interact via the nonbonded force.

where *k*_{b} and *k*_{θ} are the force constants and *r*_{0} and *θ*_{0} are the distance and angle at the minimum energy, respectively.

We have also a correction term for 1-3 interaction, which is the same as the nonbonded
(Lennard-Jones, LJ) interaction but being truncated-shifted to get zero at
.

*r*_{s} is chosen at the energy minimum distance, *r*_{min}, of LJ function. Thus, this correction term is just a short-range interaction and does not work always but effectively prevents unwilling bent structure.

Torsion potential is not typically considered, though is applied to only
selected pairs in the sterol tail;

Nonbond interaction is described by LJ functions and Coulomb interaction. Two LJ functions are used, depending on the pair of particles;

These interaction is treated by plane-cutoff scheme with the cutoff length of 1.5 nm. The coulomb interaction

should be calculated by a non-cutoff scheme like particle mesh Ewald or P3M. We set the ε

=80 to incorporate the screenning effect of water implicitly in this model.