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Bug #2187

segfault in trjconv for tpr/trr -> tng

Added by Max Linke about 2 years ago. Updated over 1 year ago.

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

I'm converting a old tpr and trr file (from 2011) into a tng. When I select the whole system the conversion works but
when I select only the protein I get a segfault. This happens in gromacs2016.3 and the master branch.

```
echo 1 | gmx trjconv -s adk_oplsaa.tpr -f adk_oplsaa.trr -o awesome.tng
```

adk_oplsaa.tpr (2 MB) adk_oplsaa.tpr Max Linke, 05/24/2017 02:17 PM
adk_oplsaa.trr (10.9 MB) adk_oplsaa.trr Max Linke, 05/24/2017 02:17 PM
run_small.xtc (113 KB) run_small.xtc Peter Kroon, 10/12/2017 12:46 PM
run.tpr (92.7 KB) run.tpr Peter Kroon, 10/12/2017 12:46 PM

Associated revisions

Revision dc4081f0 (diff)
Added by Magnus Lundborg almost 2 years ago

Update to TNG v 1.8.1

Fixes #2187 and #2250.

Change-Id: Icf81d5f3ce916e984750e1511d32e16ebc45b6f9

History

#1 Updated by Peter Kroon almost 2 years ago

I can confirm the same behaviour when using a xtc file, on both gromacs 2016.3 and 5.1.4.

It is possible to work around this, but it's very tedious.

@echo 2 | gmx trjconv -f run_small.xtc -s run.tpr -o run_small.tng

#2 Updated by Magnus Lundborg almost 2 years ago

  • Assignee set to Magnus Lundborg
  • Target version set to 2018

#3 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #2187.
Uploader: Magnus Lundborg ()
Change-Id: gromacs~master~Icf81d5f3ce916e984750e1511d32e16ebc45b6f9
Gerrit URL: https://gerrit.gromacs.org/7071

#4 Updated by Magnus Lundborg almost 2 years ago

  • Status changed from New to Resolved

#5 Updated by Mark Abraham over 1 year ago

  • Status changed from Resolved to Closed

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