[gmx-users] rotation while pulling

gromacs query gromacsquery at gmail.com
Tue Mar 28 13:37:16 CEST 2017

Hi All,

{apologies if posted multiple times; seems like some trouble with my

I want to pull linear molecule across the membrane in two ways allowing:
- translation along Z and rotation around Z
- translation along Z and rotation in all axes

My current mdp-setting pulls molecular along Z but it translates and
rotates in all axes. Do I need to use some advanced options?

; Pull Code
pull            = umbrella
pull_geometry   = direction
pull-vec1 = 0 0 -1
pull_dim        = N N Y ;
pull_start      = yes       ; define initial COM distance > 0
pull_ngroups    = 1
pull_group0     = MEM ; restrained group
pull_group1     = LIG; group to pull
pull_init1 = 0
pull_rate1      = 0.00001; nm per ps
pull_k1         = 1000       ; kJ mol^-1 nm^-2

Also in this case would it be wise to use/say absolute Z coordinate as
reaction coordinate? rather center of mass distances between membrane and


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