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

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 11 14:22:22 CEST 2006

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 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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