1M means NA number of molecules in 1 liter. 1 cubic decimeter is 1 liter. You have the box dimensions. So, from that you can calculate the concentration of the solute.

Molarity of the solute = No. of molecules / (NA x volume)

But, it is necessary to equilibrate the system first.

1M means NA number of molecules in 1 liter. 1 cubic decimeter is 1 liter. You have the box dimensions. So, from that you can calculate the concentration of the solute.

Molarity of the solute = No. of molecules / (NA x volume)

But, it is necessary to equilibrate the system first.

You can use gmx genion with -conc. Or manually you can calculate with according to box volume i.g. N = Concentration * 6.022 * box volume. Then use gmx insert-molecules command to insert calculate no of molecule.

or the oldschool method for 0.15 ionic strength:

grompp after genbox will show you the total charge of the system

then:

Y = ((number of water molecules after genbox) x 0.15) / 55.5556

if the charge is -2, for example, count of CL == Y, Na == Y + 2

add it to the genion command by using flags -np -nn and selecting the solvent molecules to be replaced with added ions

change the topology: number of waters - number of added ions, add NA CL and corresponding values...

All above answers assume that you have box of water and nothing else in it. If nothing was changed in recent versions of gromacs, genion calculates concentration in respect to the total volume, not the solvent. If you have protein or bilayer inside the system, you should take into account only water molecules. So you should calculate how many molecules should be added per one water molecule. For NaCl, using some approximations, in water it would go like this:

1 mol H2O - 18 g

1 dm3 H2O - 998 g in 25C

998/18 = 55.4 mol in one dm3 of water

Now, 1 mol of any substance is always the same number of molecules/atoms. We can safely assume that the mass of 0.15M NaCl is quite similar. If we have:

55.4 mol of water

0.15 mol of NaCl

We can say that there are 55.4 water molecules per 0.15 molecule of NaCl, so:

55.4/0.15 = 369 molecules of water/1 molecule of NaCl.

Also, since NaCl in water dissociates completely to Na and Cl, there is 1 Na and 1 Cl per every 369 molecules of water in 0.15M solution of NaCl. These rough approximations, but they are quite sufficient for MD.

Same way you can calculate number of any molecules per water.