Distance between pull groups 1 and 2 (2.877739 nm) is larger than 0.49 times
the box size (2.272821).
But my box dimension are 4.69, 4.69, 15 . Here I am pulling the drug on Z direction why does it taking directions of x and y as i am not doing anything on that direction. the smd code is as follows
pull = yes
pull_ncoords = 1 ; only one reaction coordinate
pull_ngroups = 2 ; two groups defining one reaction coordinate
pull_group2_name = DRUG
pull_group1_name = Lipid
pull-group2-pbcatom = 34491
pull-group1-pbcatom = 3903
pull_type = umbrella ; harmonic potential
pull_geometry = direction ; simple distance increase
pull_dim = N N Y
;pull_coord1_vec = 0 0 -1
pull-pbc-ref-prev-step-com = yes
pull_coord1_groups = 1 2
pull_coord1_start = yes ; define initial COM distance > 0
pull_coord1_rate = 0.00025 ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k = 100 ; kJ mol^-1 nm^-2
pull_init1 = 0