How I can calculate the number of ionic liquid molecules and the number of water molecules from a concentration of say 2M to do molecular dynamics simulation? I am thinking that my box size is 6 nm. so, total volume is 216 nm^3. From the definition of molarity I can calculate the total number of molecules which can enter into the box to maintain a concentration of say 2M. But how I will calculate the number of ionic liquid molecules and the number of water molecules separately?
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.
See related ans:
https://www.researchgate.net/post/How_can_I_calulate_the_concentration_of_a_particular_solute_in_MD_simulation_system#view=5ac24bc2c68d6ba2516c7fe1
Actually we can calculate the total number of solute molecules from the molarity definition.....(see the attached file).......but how I can get number of solvent molecules?
Saikat, you can calculate the number of solvent molecule from the density of the solution:
V ml solution of density c gm/ml
Total mass of the solution Msoln=V*c
Mass of the solute in V ml Ms = calculate from the molarity of solution
Now mass of the solvent in Vml, Msolvent= Msoln- Ms
Now you know the number of solvent molecule needed to make the solution.
But, for the simulation, I have only the molarity of the solution and the cubic box volume where I will enter the solute and solvent molecules. For the experiment purpose, I know the volume of solution......but here only the concentration(molarity) is known.........that's the problem.
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