GROMACS version: 2023.1
GROMACS modification: No
During minimization in Gromacs of the protein molecule (standard procedure for protein without any ligands) I get notification after 13th step:
[One or more water molecules can not be settled
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current cordinates.]
But then minimization continues to the 514th step when Gromacs writes lowest coordinates.
I use standard minim.mdp file with recommended for Charmm ff parametrs and integrator = steep.
Is it necessary to change something or it is Ok if minimization runs to its end?