Strange default group behavior

[Jochen Hub]

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?

Many thanks,
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: [phone]
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------

[Justin Lemkul]

Hi,
I noticed that, since gmx 4.5, some groups are twice in the default group
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
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
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
--
========================================

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

========================================

[Jochen Hub]

Post by Justin Lemkul

Hi,
I noticed that, since gmx 4.5, some groups are twice in the default group
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
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
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?

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: [phone]
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------

[Justin Lemkul]

Post by Justin Lemkul

Hi,
I noticed that, since gmx 4.5, some groups are twice in the default group
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
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
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?

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.

-Justin
--
========================================

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

========================================

[Jochen Hub]

Post by Justin Lemkul

Post by Justin Lemkul

Hi,
I noticed that, since gmx 4.5, some groups are twice in the default group
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
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
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?

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: [phone]
http://cmb.bio.uni-goettingen.de/
---------------------------------------------------