Bug #2926
gmx cluster -clndx is broken
Affected version - extra info:
Did not test 2018 versions, but suspect the same there. Also happens in master.
Affected version:
Difficulty:
uncategorized
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
Associated revisions
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
Applied in changeset ec73eb81f27cc5301054f85ae96b449a64fe8b74.
#5 Updated by Mark Abraham 4 months ago
- Status changed from Resolved to Closed
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