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Bug #133

make_ndx produces SEGFAULT with .gro files of one molecule and x1 (11, 21, 31) atoms

Added by Anonymous over 12 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

When producing an index-file from a .gro file with make_ndx I encountered the
follwing error:
Segmentation fault (core dumped);
The error is dependent on that the overall number of molecules is only 1 and
that the number of atoms in the molecule, respectively the number of atoms
indicated in the second line of the .gro file, ends with a 1 (I checked for 11,
21, 31 and 41).
I could reproduce it on three different systems for version 3.3.1; on one of
these, I checked different gromacs versions, and the problem occured for 3.3.1,
3.3, 3.2.1, but not for 3.1.4 and 3.0.5;
Here's an example how to reproduce the problem:

Use any .gro file with 1 Molecule, 11 Atoms such as the following:

DPPC
11
1DPPC NC3 1 2.824 0.625 0.874 0.2124 0.3423 -0.2272
1DPPC PO4 2 3.130 0.263 0.883 -0.1146 -0.1481 0.0779
1DPPC GL1 3 2.864 0.302 1.287 0.3450 0.0141 0.0513
1DPPC GL2 4 2.602 0.139 1.227 0.1997 0.0915 0.2110
1DPPC C1A 5 2.790 0.244 1.658 -0.0004 -0.0412 -0.0557
1DPPC C2A 6 2.981 0.130 2.030 0.3726 0.1086 0.2167
1DPPC C3A 7 3.196 0.049 2.424 -0.2474 0.5380 0.0062
1DPPC C4A 8 3.321 0.052 2.848 -0.1432 0.0688 -0.1535
1DPPC C1B 9 2.215 -0.118 1.560 0.1248 -0.1761 -0.1832
1DPPC C2B 10 2.101 -0.465 1.731 -0.1557 -0.2357 -0.2322
1DPPC C3B 11 2.282 -0.706 2.063 0.1379 0.3289 0.1055
6.27986 6.38620 8.66713

type:
"make_ndx -f xxx.gro"
select the molecule ("1")
quit and save ("q")

That should be it.

Best wishes,

Marlon

History

#1 Updated by David van der Spoel over 12 years ago

Fixed in CVS for 3.3 and 4.0

Also available in: Atom PDF