Direction of pulling using direction-periodic

User discussions
1

GROMACS version: 2019.5
GROMACS modification: Yes

Dear All,

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

Many thanks.

Best regards,
Mario

2

Sorry, the version of GROMACS does not have any modification, that was a typo.

3

Hi Mairo,

his looks okay to me - as far as I know, there is no way to specify this type of pull coordinate explicitly. Note that you will have take care of the ref-coord scaling when using pressure coupling during your simulations.

4

Many thanks!