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Bug #1662

g_hbond not running

Added by Antoni Borysik over 2 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
analysis tools
Target version:
Affected version - extra info:
GROMACS 4.6.7
Affected version:
Difficulty:
uncategorized
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Description

Hi, have run various vacuum simulations with GROMACS 4.6.7. I find I can calculate h-bonds using g_hbond -f md.trr -s md.tpr on some simulations just fine while on others the system freezes 'Frame loop parallelized with OpenMP using 32 threads' even after leaving > 12 hours there is no progress or error. I have not found this problem on the web nor been able to sort out myself. I have tried various -nthreads flags including 1 and it wont budge. I get no error report it just freezes -> any insight would be most appreciated.

Associated revisions

Revision aa1cfd57 (diff)
Added by Erik Marklund about 2 years ago

gmx hbond no longer removes PBC when none is present

Fixes #1662

Change-Id: Ice934285784ac8b8fd95942a089fb1b65b9ecb51

History

#1 Updated by Erik Marklund about 2 years ago

  • Assignee changed from Antoni Borysik to Erik Marklund

#2 Updated by Erik Marklund about 2 years ago

I think this is related to the absence of pbc and I can reproduce this with other gas-phase trajectories. (Why doesn't g_hbond have the -nopbc option btw?) Will dig deeper.

#3 Updated by Erik Marklund about 2 years ago

  • Target version changed from 4.6.8 to 5.0.5
  • Affected version changed from 4.6.7 to 5.x

The bug is there in release-5-0. I'll fix it and try to backport to release-4-6.

#4 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #1662.
Uploader: Erik Marklund ()
Change-Id: Ice934285784ac8b8fd95942a089fb1b65b9ecb51
Gerrit URL: https://gerrit.gromacs.org/4350

#5 Updated by Mark Abraham about 2 years ago

  • Subject changed from h_hbond not running to g_hbond not running

#6 Updated by Mark Abraham almost 2 years ago

  • Status changed from New to Closed

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