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.
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