GROMACS version: 2021.4-Ubuntu-2021.4-2
GROMACS modification: No
does anyone here know if it is possible to initialize a surface with explicit surface roughness?
I have already given a surface where depending on position restraints, the individual atoms can move and consequently the surface changes within fixed limits.
However, I would like to fix the position restraints and set the roughness manually to a fixed value, so that it cannot change any more/or only very slightly in order to be able to compare input parameters better.
Is there a special program where I can specify atoms or even a base area and then the coordinates are adjusted accordingly, so that a predefined roughness is created?
Or is this even possible in Gromacs? So far I have only read about the “gmx sasa” function, although in my opinion this cannot be used for initialization, but only for analysis.
I am grateful for any information!