What matters is not the mass concentration - You need to calculate the molar concentration by dividing the mass concentration by the molecular mass of the ligand. Molar concentration times Avogadro's number per mole gives you the number of molecules in a given volume. Adjusting the volume to the size of the solvent box in your simulation, you can calculate the number of ligand molecules you need to place into the solvent box to achieve the desired concentration.

You can make following M = n/V ; where M is molarity (i.e. 0.5 M or 500 mM). n is number of moles that you need calculate, V is volumen (box volumen x*y*z lenght in A^3 convert to Liters), them n (number of moles) is multiple for avogadro number (An), example: numer of molecules to be placed (np) is : np = n * An. is is more clasical aproximation. For other hand, you can calculate number of moles using 50 ng/ml, with n = mass / molecular mass (it is ligand molecular mass) and after it make n * An is equal to number of molecules to be placed into box simulation. Keep into mind that you can add repulsión forces to avoid ligand aggregation.

Annemarie Honegger Ropón-Palacios G. Can i ask again. in gromacs, on the step which added the ligand mass and how to add it?

You just pre-calculate how many ligand molecules go into your solvent box using a pocket calculator, no need to bother the simulation programs for that. Then add the pre-calculated number of ligand molecules to your system. Depending on the size of your system, this number will probably be in the single digits.

Annemarie Honegger thankyou very much. Im helpfull