Hi there,

I want to calculate the exact concentration of ions in the box. Could anyone please help me do it?

Here is my information:

cubic box with -d 2.0

SOL 42909

MG 100

CL 143

Concentration is moles per liter. You know how many ions you have and you know the size of your box (we don’t because you didn’t tell us). You therefore have everything you need.

If you have large solutes, you need to subtract their excluded volume (not trivial, but I think `editconf`

can print this out).

Thanks for your response.

Do you mean the number of ions in the box is considered as a mole?

For example here, in the topology file, I have 100 moles Mg and 143 moles Cl?

Note that there is a difference between a mole and a molecule. Please consult a basic chemistry textbook about the difference and how to do the calculation if you are still confused about what to do.

Thanks, I am still confused, because I don’t know ions in my box are considered as a mole or not?!!

A mole is 6.022 x 10^{23} of something. If conversion between molecules and moles is not intuitive to you, I would echo the advice above to revisit some basic chemistry texts. Solving this kind of problem is not really pertinent to GROMACS.

Thanks, dear doctor. I have solved my issue with your guidance.