Distortion structure after energy minimization

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)

Hi Sam,

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.

If you use

gmx trjconv -s {your.tpr} -f {confout.gro} -pbc whole

you should see the expected outcome.

thanks for replying and helping :-)