[gmx-developers] Strange default group behavior

[Justin Lemkul]

On 8/20/12 1:23 PM, Jochen Hub wrote:
> Hi,
>
> I noticed that, since gmx 4.5, some groups are twice in the default group
> selection. For example, I have a pdb file with residues SOL, HEX, SOQ and NA:
>
> ATOM      1  C1  HEX     1      22.920  23.660  65.120  1.00  0.00      C
> ATOM   5688  MW  SOL  1182       8.140   7.030   0.760  1.00  0.00
> ATOM   5692  MW  SOQ  1183      21.970  25.660   4.180  1.00  0.00
> ATOM   5693  NA  NA   1184      10.010   5.080   4.740  1.00  0.00
>
>
> The default groups are:
>
>    0 System              :     4 atoms
>    1 Other               :     2 atoms
>    2 HEX                 :     1 atoms
>    3 SOQ                 :     1 atoms
>    4 NA                  :     1 atoms
>    5 Water               :     1 atoms
>    6 SOL                 :     1 atoms
>    7 non-Water           :     3 atoms
>    8 Ion                 :     1 atoms
>    9 HEX                 :     1 atoms
>   10 SOQ                 :     1 atoms
>   11 NA                  :     1 atoms
>   12 Water_and_ions      :     2 atoms
>
> The problem is now, that make_ndx and other tools throw an error if I try to
> select the group "HEX":
>
> Error: Multiple groups 'HEX' selected
>
> This is a very annoying behavior in scripts where different groups don't always
> have the same group number, so one wants so select a group by its name.
>
> Btw, the problem disappears if one removes the "NA" line from the PDB file,
> which is even stranger.
>
> Is this an intended behavior or should I file a redmine?
>

It's probably related to this issue:

http://redmine.gromacs.org/issues/490

Perhaps we need to re-open that one rather than start a new issue report.  I 
have always thought that the multiple groups was somewhat inconvenient, but 
never had an error arise from it.  I'm assuming you're only selecting one group 
when prompted?  The groups are redundant, but in theory, you can fill any index 
file with junk numbers with whatever names and you can select any viable group.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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