[gmx-users] PMF calculation: molecule though the channel.

[Nikhil Maroli]

Dear all,

Im trying to pull water molecules through Aquaporin channel with the
following pull parameters (to obtain PMF). On visualising the trajectory,
water molecules travelling around the surface/outside of aquaporin instead
of going through inside. How I can make sure that the water molecule is
going through the channel, I tried different values of k, pulling rate and
kept water at the top and the middle region (inside) of the channel, still
it is not travelling though the channel.

pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_B
pull_group2_name        = Chain_A
pull_coord1_type        = umbrella
pull_coord1_geometry    = direction-periodic
pull_coord1_groups      = 1 2
pull-coord1-vec = 0 0 1
pull_coord1_rate        = 0.1          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 100
pull_coord1_start       = yes


I would be appreciative of any suggestions



-- 
Regards,
Nikhil Maroli