GROMACS version: 2020.4
I got a distorted structure for my dithiol cyclic structure after nvt equilibration so I decreased the number of steps but the issue still exists.The step of energy minimization couldn’t be completed as it always stops on the thiol atoms and I tried to increase the maximum force but also didn’t success
Energy minimization reached the maximum number of steps before the forces
reached the requested precision Fmax < 10.
writing lowest energy coordinates.
Steepest Descents did not converge to Fmax < 10 in 10001 steps.
Potential Energy = -7.7265070e+02
Maximum force = 9.2542824e+01 on atom 141
Norm of force = 1.1121471e+01
GROMACS reminds you: “Life need not be easy, provided only that it is not empty.” (Lise Meitner)
Overall, this looks like a good result from the energy minimisation. Even though you do not end up with an F_{max}<10 , your maximum force is not so far of. You can have a look at the energy with gmx energy to check if there is anything unusual happening, if you see a flattening potential energy curve that is almost level, you should be okay to start running your simulation.
This looks very much like a periodic boundary condition thing - nothing wrong with the physics of the system but a matter of visualisation.
