Hi Deniz,
Note that this is a common issue ( see https://gromacs.bioexcel.eu/search?q=lincs )
Lincs warnings are usually pointing to an instability in the system; your system is not well enough equilibrated. There are a number of things you can do:
- decrease your simulation time step to 1fs for an additional equilibration
- use another thermostat for equilibration (v-rescale)
- use another barostat for equilibration (Berendsen for equilibration purposes only!)
- slowly warm up your system with simulated annealing
- manually inspect and fix the stereochemistry where the lincs warnings occur
You might find more suggestions in the search link above.