GROMACS version:2018
GROMACS modification: Yes/No
I want to md simulate an enzyme with a metal ion. My enzyme system should be simulated keeping no,of molecules, pressure and temperature constant. So how can we determine the concentration of the metal ion we use in the simulation using the no.of metal ions we add to the system since our system has varying volume with time?
For example what could be the concentration of Na+, if we add 2 Na+ ions to the enzyme system that contain total of 36480 molecules along with water. (PS:These are imaginary values and not relevant to my simulating system)
If you want a specific concentration, I would suggest generating your system (first without the metal ions), energy minimize and run a short equilibration (NVT followed by NPT) just to find the approximate volume of your system. Then you can insert (or add) your metal ions to get the concentration you want. If you find that the system is too small to accurately enough get the concentration you need, you should probably be able to deduce approximately how large simulation system you would need.
You must also keep in mind if the concentration you want is the concentration in water or if it is the concentration in the system volume (water + protein in your case). If it is the concentration in water you want to reproduce, you do not need the protein in the system in the procedure I described above.
I hope that helps.