Many problems are resolved by carefully reviewing the output log file; you will need to learn how to do this if you wish to advance.
Besides what Lennart has already noted, I should point out a couple errors in the input:
- The TCONS keyword conflicts with and overrides the HOOVER keyword, and invokes the older, flawed Berendsen thermostat; you should remove the TCONS keyword.
- The system may have a net non-zero charge with Ewald, which is not recommended, esp. for a beginner, as QCOR 0.0 is probably not the best choice for that. In general, for a system with ions, both cations and anions should be included, and their charges should sum to zero.
- You appear to be trying to read a restart file via IUNRE 49, but do not specify RESTART in the DYNA command.
Why read two coord sets, instead of just reading water_ions_min.crd in the first place?
Also, for a beginner, the hydronium ion seems like a poor choice; its lifetime is so short that it is not part of the standard parameter distribution.
Your HMCM command restrains the ions to a corner of the box, and not the center (0,0,0), which seems exceedingly odd.
Since you do not appear to be using the DOMDEC feature, you could use MMFP GEO PLANAR restraints to keep the ions instead the box, but the use of restraints for production MD is highly discouraged, as they perturb the system and must be accounted for during later analysis.
Overall, this is a problematic script with a problematic choice of a simulation system.