GROMACS version: 2023.3
GROMACS modification: Yes/No
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Based on gromacs Protein-ligand complex tutorial to run MD simulations and The step of Adding ions in an added ion but the step shows No ions to add, will just copy input. After am continuing MD simulations later am got the error is it not shows water-ions option in index file? Can you please give me the suggestions to solve it,
You are requiring a number of ions that can neutralise the system and no specific concentration on top of that. In this case GROMACS should just try to put the number of ions needed so that the total charge of your system is zero. I think the answer from gmx genion is telling you that the total charge is zero already and that there are no things to do, i.e., no ions to add.
If you want a specific concentration you should also add the -conc flag.
Thank you obZehn! Am take -conc 0.06 option in that command after 3 CL and 3 NA ions are identified. It worked and once again thank you.
