Pull code distance restraint

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1

GROMACS version:2022.5
GROMACS modification: no
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Hi,

I want to simulate a protein-ligand system, and I would like to keep the small molecule within a certain distance from the protein. To do so, I would like to define centres of mass for the ligand and the protein and then define the distance parameters I want to maintain between these two centres of mass.

Let’s say that I want to define the COM of atoms 600 and 602 (they belong to the protein) and the COM of atoms 400 and 402 (ligand atoms), and have a potential (a flat bottomed one I guess in my case) kick in only when their in-between distance exceeds 3 angstroms. I have read that the pull code can be called in the mdp file and then gmx mdrun will know what to do with it. However, checking the pull code manual left me with more questions than answers as I got really confused regarding how I am supposed to set up the syntax. I know that a plumed plugin can also deal with this problem, but I would prefer avoiding calling plumed for now since it would strike a hit on the simulation performance.

Any help will be greatly appreciated.

2

Something like this (might contain typos):

pull                     = yes
pull-ncoords             = 1
pull-ngroups             = 2
pull-group1-name         = "put in name of group 1"
pull-group2-name         = "put in name of group 2"
pull-coord1-type         = flat-bottom
pull-coord1-geometry     = distance
pull-coord1-groups       = 1 2
pull-coord1-init         = 0.3
pull-coord1-k            = 1000.0 "maybe a larger force constant is needed"
3

Perfect! Thank you very much!!!