[gmx-users] ions coupl to protein in .top

[Mark Abraham]

zhong qiang wrote:
> Hi :
> 
>      I have four calcium ions in .top file, But when I run grompp -f 
> fullmd_sol.mdp -c minimized_water.gro -p cln.top -o fullmd.tpr
>    The Error report:
> Fatal error:
> 4 atoms are not part of any of the T-Coupling groups

Temperature coupling groups are defined in the .mdp file... you should
be using "Protein Non-Protein" rather than the "Protein SOL" you
probably are using. Note, do not couple these handful of ions in their
own coupling group.

Mark