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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
