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

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 11 16:00:20 CEST 2006

Una Bjarnadottir wrote:
> 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?
> tc-grps':'Protein OTHER CL-  ###where I have to call SOL: OTHER 
> otherwise error
>>> 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.
> I made the indes file after running genion using the .gro output file 
> from genion generating it.  Also I thought you would have to subtract 
> one and it was groups 14 and 0 instead of 15 and 1.  How would I have 
> the ions part of the solvent T coupling group?  By modifying the .top 
> file to [ molecules ]
> ; Compound        #mols
> Protein_E           1
> Protein_I           1
> Protein_A           1
> SOL+CL-          9719
> and than the tc-grps in the .mdp file accordingly to that.  How will I 
> define SOL and CL- together, I tryed SOL+CL- and SOL-CL- but Fatal 
> error: No such moleculetype SOL+CL- came for both.
> Best regards David for your reply, Una David.

in make_ndx you type
14 | 15
that will give you the combination of the two groups (if 14 is SOL and 
15 is CL-)

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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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