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

[David van der Spoel]

Una Bjarnadottir wrote:
> 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)
> 
> which is the last water atom (total in system 33003) and groups 15 and 1 
> are Cl and protein groups if I on the other hand do not neutralize the 
> system the run goes fine!  When looking into the .ndx file atom 33000 is 
> in 4 groups;  0 (system), 11 (non-protein), 14 (SOL) and 16 (other).  
> How can I change the group definitions and make sure the groups do not 
> overlap and to be unique?
> It seems to be something wrong with how the genion works for me.  I 
> followed the tutorial and chose the SOL group and water molecules were 
> replaced by the Cl ions.  Than I modifyed the .top file and took 3 sol 
> molecules and added the 3 ions.
> 
> Please help because have not been able to fix the problem with related 
> letters on the subject on the list.
> 
> Best regards, Una Bjarnadottir
> 
What do your tcoupl groups look like?

Could it be System SOL?

The number may be confusing, you should subtract one from them when 
compared to the output from gmxcheck -n index.ndx
So it seems that atom 33000 (numbering in the coordinate file) is in 
groups 14 and 0. Maybe you should make a new index file after genion.
Note that it is good practice to make the ions part of the solvent T 
coupling group.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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