[gmx-users] genion causing atom to be in multiple T-Coupling groups

[Mark Abraham]

> Dear Users,
>
> I'm hoping for an answear on my problem with neutralizing my system
adding
> 3 Cl ions with genion.  When
> running grompp after genion with the new generated .gro file I get this
error:
>
> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)

Read closely - "T-Coupling group", not "group". You choose the T-Coupling
groups from among those in the .ndx file (or from the default groups in
its absence, as you're doing here) and specify them in the .mdp file. Thus
you should look there first of all. You need to use a disjoint set of
T-Coupling groups, so this error is consistent with not having done that.
If you were using .ndx file (which you aren't), it might be possible your
.ndx file doesn't correspond to your post-genion structure and something
weird happens. I'd expect GROMACS woud die with a more helpful error in
such a case though.

Mark