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

Una Bjarnadottir una.bjarnadottir at ucd.ie
Mon Sep 11 15:58:56 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?

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 

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