59
pull_group2_name = CD
pull_coord1_type = umbrella ; harmonic potential
pull_coord1_geometry = distance ; simple
distance increase
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM
distance > 0
pull_coord1_rate = 0.01 ; 0.01 nm per ps =
10 nm per ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
In the above code we ask the program to perform a pulling
simulation (pull=yes) and we impose one reaction coordinate. We
define two different groups (CC and 2-HP-B-CD in this case) by
imposing a harmonic potential (pull_coord1_type=umbrella). We
choose to pull as per distance (different options such as direction
are available; for further alternatives see  Note 6). The next code
line (pull_coord1_dim= N N Y) specifies that the pulling will take
place only to the z-direction with N standing for No and Y standing for Yes. The reaction coordinate connects groups 1 and 2 and
the first COM distance is the reference distance for the first frame.
Fig. 9 The CAN:2-HP-B-CD complex. The CAN molecule (green highlight) will be
pulled out of the cavity through CD’s wide rim
Study of Candesartan Cilexetil: 2-Hydroxypropyl-β-Cyclodextrin Interactions…