1. Sounds good until here. You should make sure you are using good parameters for the ions, f.i. regarding solubility, there were some improvements over the standard counter ion parameters which are shipped with most forcefields. So the choice of FF is critical here regarding solute or ionic liquid representation.

3. This depends on the method you want to use for the binding free energy calculation. The most common options are Thermodynamic Integration (FEP/TI) or MMGBSA. The 1st option is rather difficult to do right, even for people being trained in MD techniques. The latter is quite easy to do but its not clear if the implicit solvent will correctly represent your ionic liquid even with the corresponding setting for the ion concentration.

4. For instance NAMD/VMD or GROMACS.

Dear Debashish,

I have not tried molecular dynamics simulation myself ever but I have gone through relevant literature by other researchers during my doctoral research.

If I recall it right the force field suggested for simulating ionic liquid systems is OPLS-AA. 

Current trend in ionic liquid simulations however suggests that the best way is Ab Initio Molecular Dynamics.

Please think with this angle. 

As far as I understand through my experience with Ionic Liquid systems, explicit solvation is the ideal way having atleast 4 ion pairs.

What ILs and solvent(s) are you using? OPLS and GAFF provide generally good properties for a variety of ILs but many are better parameterized with specific force fields.