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Bug #2926

gmx cluster -clndx is broken

Added by Paul Bauer 4 months ago. Updated 4 months ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
Affected version - extra info:
Did not test 2018 versions, but suspect the same there. Also happens in master.
Affected version:
Difficulty:
uncategorized
Close

Description

During writing tests and replacing the functionality I noticed that it seems to be broken during the creation of the underlying datastructure.
Test case files are attached.
Commandline used was

gmx trjconv -sub clusters.ndx -f traj.trr -o test.xtc

Clusters where prepared from traj.trr using this command
gmx cluster -clndx -f traj.trr -s topol.tpr -n spc-dimer.ndx -cutoff 0.0015

traj.trr (8.53 KB) traj.trr Paul Bauer, 04/15/2019 04:07 PM
clusters.ndx (311 Bytes) clusters.ndx Paul Bauer, 04/15/2019 04:07 PM
topol.tpr (16.5 KB) topol.tpr Paul Bauer, 04/15/2019 04:07 PM
spc-dimer.ndx (41 Bytes) spc-dimer.ndx Paul Bauer, 04/15/2019 04:07 PM

Associated revisions

Revision ec73eb81 (diff)
Added by Paul Bauer 4 months ago

Fix off-by-one error in gmx cluster

The writing of indices for linking frames to clusters was of by one.

Also fixed naming to refer to indices and not indexes

Fixes #2926

Change-Id: I67d7f8cae56734e425c84460080de8896f6239cb

History

#1 Updated by Paul Bauer 4 months ago

  • Subject changed from gmx trjconv -sub seems to be broken to gmx cluster -clndx is broken -sub seems to be broken

#2 Updated by Paul Bauer 4 months ago

  • Subject changed from gmx cluster -clndx is broken -sub seems to be broken to gmx cluster -clndx is broken

The bug is actually in the generation of the index file in gmx cluster.

#3 Updated by Paul Bauer 4 months ago

  • Target version set to 2019.2

#4 Updated by Paul Bauer 4 months ago

  • Status changed from New to Resolved

#5 Updated by Mark Abraham 4 months ago

  • Status changed from Resolved to Closed

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