GROMACS version: 2021
GROMACS modification: Yes/No
I have a box of 7x7x7 nm filled with 11225 water molecules. I tried to use genion to add 300 Ca2+ and 600 Cl- to have a cacl2 solution but I got the error: No more replaceable solvent!
Here is the command: gmx genion -s ions.tpr -p topol.top -o calcl2.gro -np 300 -pname CA -pq 2 -nn 600 -nname CL -nq -1
I think I have sufficient replaceable water for only 900 ions. Can anyone help me with this issue? Thanks.
gmx genion is looking at ‘the water molecules available for replacing’. Those water molecules are at a distance larger than minimum distance between ions and non-solvent (defined by rmin). If this group is empty, it prints " No more replaceable solvent!
I guess that this may be the issue you met. You can try to change the values of rmin to see the effect. Note, changing the values of rmin may be dangerous since you can get steric clash between ions or a water molecule-ion if this parameter is not fine tune.
You can also try the option -conc
Thanks so much for your reply. I adjusted the rmin and it worked!