[gmx-developers] Strange default group behavior

[Jochen Hub]

Am 8/20/12 7:35 PM, schrieb 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.

Hi,

I don't really understand "only selecting one group when prompted?" 
here. It seems that Gromacs does not allow the selection of a group 
using the group name *if* several groups have the same name.

If the groups would "only" be redundant the double groups would not be a 
problem. The problem is that the group selection does not work properly 
this way.

Cheers,
Jcohen




-- 
---------------------------------------------------
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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