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Bug #189

g_hbond does not work

Added by Esteban Voehringer-Martinez over 11 years ago. Updated over 11 years ago.

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

Hi,

I tried to use the g_hbond tool from the version 3.3.3 from the web page on a Linux machine. The compilation and installing of gromacs went without any problems and all the other tools work fine. Only g_hbond is not working.
I'm simulating spc-water at 300K and 1 bar with SETTLE algorithm Berendsen pressure and temperature coupling. The trajectory and the tpr file is made also with version 3.3.3.
I ran the debugger and I get a Segmentation fault in function "is_hbond" with option -num and in function "add_ff" when -num and -ac is set.
I asked already David van der Spoel and he suggested to submit a bug.

Esteban Voehringer-Martinez

History

#1 Updated by Erik Marklund over 11 years ago

(In reply to comment #0)

Hi,

I tried to use the g_hbond tool from the version 3.3.3 from the web page on a
Linux machine. The compilation and installing of gromacs went without any
problems and all the other tools work fine. Only g_hbond is not working.
I'm simulating spc-water at 300K and 1 bar with SETTLE algorithm Berendsen
pressure and temperature coupling. The trajectory and the tpr file is made also
with version 3.3.3.
I ran the debugger and I get a Segmentation fault in function "is_hbond" with
option -num and in function "add_ff" when -num and -ac is set.
I asked already David van der Spoel and he suggested to submit a bug.

Esteban Voehringer-Martinez

Hi,

I am fixing a memmory issue in g_hbond which is is_hbond()-related. Could you upload the tpr/trr files so I can check whether my fix also fixes your problem?

/Erik Marklund

#2 Updated by Erik Marklund over 11 years ago

I've fixed some serious writing-outside-of-the-array-issues. This was most likely the source of the reported segfault.

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