[gmx-users] Pull Code: direction-periodic with 3 dimensions

[Daniel Kozuch]

Hello,

I am using a pull code to increase the end-to-end distance of a protein
(included below). I am using direction-periodic and would like the distance
between the COM groups to be calculated in three dimensions. However,
setting pull_coord1_dim = Y Y Y appears to have no effect and the distance
printed to the pull file is still only in the pull_vec dimension (as
verified by checking with gmx distance). Is there any way to use
pull_coord1_dim = Y Y Y with direction-periodic?

pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_Begin
pull_group2_name        = Chain_End
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = direction-periodic
pull_coord1_groups      = 1 2
pull_coord1_dim         = Y Y Y
pull_coord1_rate        = 0.0
pull_coord1_k           = 5000          ; kJ mol^-1 nm^-2
pull_coord1_start       = no           ; define initial COM distance > 0
pull_coord1_init = 3.5
pull_coord1_vec         = 0 0 1


Thanks,
Dan