GROMACS version: 2019.5
GROMACS modification: Yes
I am trying to arrange a pulling simulation of a protein using an umbrella potential and direction-periodic.
I was wondering how I can impose the direction of the pulling to be along the longest diagonal of my rectangular box?
I was assuming this could be done setting pull-coord1-vec as the vector that one can find at the bottom of the gro file used by the pulling code. Is this correct? Is there any other way?
In any case, I am leaving here the pulling part of my mdp file:
indent ppull = yes
pull-coord1-groups = 0 1
pull-group1-name = ProteinC
pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-vec = 39.70966 5.95645 5.95645
pull-nstxout = 1000
pull-nstfout = 1000
pull-group1-pbcatom = 1200
pull-pbc-ref-prev-step-com = yes