GROMACS modification: No
Question- Can we use default mdp parameter files present online for all proteins and protein-ligand complex? If no, how will set the parameters and its values?
No. Each force field has its own requirements for appropriate cutoffs, treatment of constraints, long-range corrections, etc. The defaults provide a plausible set of values that may be suitable but you should not assume these values are valid for any particular purpose. You need to understand the force field you’re using and assign the settings appropriately.
Ok. I will do a research on selecting parameter values. Again thank you.