How do I pull two protein units each in rotation?

User discussions
1

GROMACS version: 2018.4
GROMACS modification: No
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I want to pulling while rotating two units at the same time with their respective rotating shafts, but only one pull-coord1-vec option is applicable. What should I do?

pull-coord1-type = umbrella
pull-coord1-geometry = angle-axis
; Select components for the pull vector. default: Y Y Y

; Switch from r1 to r0 in case of dynamic reaction force
pull-coord1-vec = 0.055499 0.0249185 -0.9918185
pull_constr_tol = 1e-06
pull-coord1-start = no
pull_nstxout = 100
pull_nstfout = 100
; Number of pull groups
pull_ngroups = 2
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull-group1-name = Protein_A
pull-group2-name = Protein_B
pull-coord1-groups = 1 2
pull-coord1-init = 90
pull-coord1-rate = 0
pull-coord1-k = 1000
pull-coord1-kB = 1000

2

Hi Yenju,

Using more than one pulling coordinate should help you here. Set pull-ncoords = 2 and then set all values for pull-coord2-type accordingly.

Best,
Christian

3

I really appreciate your reply!

Thanks again.

Yeonju.