GROMACS version: 2020.1
GROMACS modification: Yes/No
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Hi GROMACS users,
When we use pdb2gmx, it automatically gives us a position restraint itp for our system. If special position restraints [.itp file] are required, one can use genrestr utility of the gromacs. I want to apply a flat-bottom position restraint on a water layer in z+ and z- directions. There are other molecules also in the system but they are above and below the water layer. The thickness of water layer is 1 nm. As much I understood, the format of the flat-bottom position restraint for water would be as following:
; Position restraint for each water oxygen
[ position_restraints ]
; i funct g r k
1 2 5 0.5 1000
where funct = 2 will ensure the flat-bottom potential, g = 5 will ensure its applicability only in the z-direction, r = 0.5 is the half-width of the flat-bottom potential, and k = 1000 is of course force constant. Possibly, this itp will apply force on water molecules if any water molecule is below [COM_water (z) - 0.5] nm or above [COM_water(z) + 0.5] nm, where COM_water(z) is the center of mass of the water molecules.
Now my question is following:
I wrote the above itp by hand. Is it possible to get this itp by “gmx genrestr” utility or by other utility of GROMACS? In the present example, I have water. So it is easy to write it by hand. But other complex system, it might be difficult. I don’t see any option in genrestr to define function type etc.