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

[Tsjerk Wassenaar]

Una,

In your case you can also try the T-coupling groups Protein and
Non-Protein, without providing a .ndx file. However, in general give
some thoughts to temperature coupling (groups) when setting up your
system and try to grasp how groups are treated in gromacs.

Hope it helps,

Tsjerk

On 9/11/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> ________________________________________________________________________
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336