  A self activated siphon, which is also known as self-siphon or self-priming
siphon, is simulated using molecular dynamics (MD) method in order to study its
behavior, especially why it has a critical height that prevents fluid from
flowing through it. The trajectory of the fluid interface with air in front of
the flow or the head is also fitted the trajectory modeled by parametric
equations, which is derived from geometry construction of the self-siphon.
Numerical equations solved using MD method is derived from equations of motion
of the head which is obtained by introducing all considered forces influencing
the movement of it. Time duration needed for fluid to pass the entire tube of
the self-siphon, {\tau}, obtained from the simulation is compared
quantitatively to the observation data from the previous work and it shows
inverse behavior. Length of the three vertical segments are varied
independently using a parameter for each segment, which are N_5, N_3, and N_1.
Room parameters of N_5, N_3, and N_1 are constructed and the dependency of
{\tau} to these parameters are discussed.
