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

Nikhil Maroli scinikhil at gmail.com
Thu Sep 14 14:07:04 CEST 2017

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

Nikhil Maroli

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