Using different ions fro simulation

User discussions
1

GROMACS version: 2018
GROMACS modification: Yes/No

Hi,

I was wondering if there is a way to add two types of ions (e.g. Na+CL-, Ca2+) in one simulation if different concentrations 150mM and 1mM respectively in a single system? I want to simulate a protein that requires both the ions for activity in the experimental setup.

Thanks and regards,
Subhom

2

Hi Subhom,

Yes, that works with two different strategies:

Either you run gmx genion two times or you use gmx insert-molecules to randomly place, e.g. the Ca2+ ions.

The insert-molecules path is faster, because you don’t need to re-create a tpr file and make sure lines are added correctly in the .top file, but it will not check if the ion placement was done with reasonable spacing to protein or other ions - for that you will have to run genion, generate a tpr, then run genion again.