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Bug #1561

multiple xtc-groups: only first group written out in .xtc file

Added by Johannes Wagner over 2 years ago. Updated over 2 years ago.

Status:
Closed
Priority:
High
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

I specified 2 xtc-groups, protein and ion and grompp'd without index file. The resulting .xtc trajectory gets loaded on a pdb coordinate file (including both groups) and vmd does not report a missmatch of atomnumbers between coordinate and trajectory.
But, after the first coordinate frame, ions are not visualized anymore, instead one ion is displayed, always fixed at the box edge (0,0,0).

Associated revisions

Revision 40047094 (diff)
Added by Erik Lindahl over 2 years ago

Fix selection of xtc groups not starting at index 0

The code to select atoms to write to the xtc file
only looped over the number of atoms selected for
output rather than all atoms. This meant that xtc
group selections that were not located at the start
of the atom indices would not be written correctly.

Fixes #1561.

Change-Id: I48886a75c682e38122dadcb2f752507b14b308fe

History

#1 Updated by Johannes Wagner over 2 years ago

sorry, title is a bit misleading. both groups are written out. but the second group is not properly written out...

#2 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #1561.
Uploader: Erik Lindahl ()
Change-Id: I48886a75c682e38122dadcb2f752507b14b308fe
Gerrit URL: https://gerrit.gromacs.org/3827

#3 Updated by Erik Lindahl over 2 years ago

  • Status changed from New to Fix uploaded
  • Assignee set to Erik Lindahl

#4 Updated by Roland Schulz over 2 years ago

  • Status changed from Fix uploaded to Closed

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