[gmx-developers] Strange default group behavior

[Jochen Hub]

Am 8/21/12 11:33 AM, schrieb Justin Lemkul:
>
>
> On 8/21/12 5:11 AM, Jochen Hub wrote:
>>
>>
>> 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.
>>
>
> I see the problem now.  Can you select the desired group by its number
> rather than its name?  That should be a viable workaround while waiting
> for a fix.

Yes, the number works (and one can pick it with a few extra lines in a 
script). So as you said, this is a viable workaround.

Jochen


-- 
---------------------------------------------------
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/
---------------------------------------------------