Fatal error while executing genion at add ion concentration

User discussions
1

GROMACS version:2022.2
GROMACS modification: No

@jalemkul
upon executing gmx genion -s ions.tpr -o test_solv_ions.gro -p topol.top -pname NA -nname CL -conc 0.15 -neutral I selected 1 for protein
it gives the following fatal error

Fatal error:
Your solvent group size (3621) is not a multiple of 16

How to deal with it?
Thanks

2

You need to select solvent molecules for replacement. See basic tutorial material, e.g. Lysozyme in Water

3

@jalemkul Thanks

I have been following the same tutorial and I have executed the following commands in order before executing the gmx genion command.

gmx editconf -f test.gro -o test_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp test_newbox.gro -cs spc216.gro -o test_solv.gro -p topol.top
gmx grompp -f …/mdp_files/ions.mdp -c test_solv.gro -p topol.top -o ions.tpr

Please guide me if I need to make some changes in mdp files?

4

The problem you’re facing has nothing to do with .mdp settings (which are irrelevant for running genion, anyway). You just need to make a sensible selection for replacing solvent with ions.