GROMACS version: 2020.x
GROMACS modification: Yes/No
I am setting a system similar to https://pubs.acs.org/doi/10.1021/acs.jctc.5b00499 where the atomistic (AA) waters are surrounded by CG water. In order to avoid the AA water to mix with the CG solvent harmonic restraints are imposed to keep them together.
Reading the manual (http://manual.gromacs.org/current/reference-manual/functions/restraints.html) I think the (attractive) sphere flat-bottomed position restraints are appropriate for my problem since I want they are applied when the molecules get too close to the boundary.
Earlier in the manual, it states “For spherical shells, it is a wise procedure to make the force constant depend on the radius, increasing from zero at the inner boundary to a large value at the outer boundary. This feature has not, however, been implemented in GROMACS.” Is there an example on the .mdp options to implement this in 2020.x versions? They use Gromacs 4.6.5 in the previous paper.
Thanks in advance.