Hi Garims,

The steps for adding the ions in gromacs simulation box is well described in tutorials by Dr. Justin Lemkul, you can follow it here:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/04_ions.html

For calculating the number of ions, I think sometimes if your box is very small and also the concentration of ions is small, then the calculations turn out to be only let's say 0.1 or 0.2 number of ions. In that case I would not add any ion to my system. Otherwise if the system is not neutral, then I would just add enough number of counter ions to keep the net charge of the system equal to 0

Best,

Swapnil

@Swapnil. I have to do Calcium induced simulation studies so for this, I have to add Calcium ions to my system. I want to know the how to calculate the number of calcium ions to add for 1mM, after the waterbox.

How many number of Ca so you get when you do the calculations?

What is the size of your box?

Water concentration is ~55.5 M. If you want to have 0.001 M concentration of calcium ions, add one calcium ion for every (55.5 / 0.001) = 55,500 water molecules.