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Bug #2604

gmx msd appears broken in master

Added by Kevin Boyd over 1 year ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
analysis tools
Target version:
Affected version - extra info:
Does not affect release 2018
Affected version:
Difficulty:
uncategorized
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Description

gmx msd results in a bunch of nans. The first value (lag = 0, so msd=0) is fine, as is the second. From the third on are nan.

Reproduced with multiple option combinations, with different systems on different machines. Release 2018 is fine.

Uploaded an example of a cg water system. gmx msd -f topol.xtc -s topol.tpr

topol.tpr (16.6 KB) topol.tpr Kevin Boyd, 08/13/2018 02:59 AM
topol.xtc (693 KB) topol.xtc Kevin Boyd, 08/13/2018 02:59 AM

Associated revisions

Revision cc9b3962 (diff)
Added by Roland Schulz over 1 year ago

Fix MSD

Fixes #2604

Change-Id: Ie0f1bb881d8ba1b5cc363c3645130123245c98a6

History

#1 Updated by Roland Schulz over 1 year ago

Can you provide sample input and arguments which give the error? Could you also run "git bisect" to find the commit which produced the error? Should be fast given that there are few commits which changed gmx_msd.

#2 Updated by Kevin Boyd over 1 year ago

From git bisect, the change that broke it is commit 8517dc152f402d538c58061d44f849b1a1102e6b , which didn't actually change anything in the msd code

#3 Updated by Kevin Boyd over 1 year ago

From git bisect, the change that broke it is commit 8517dc152f402d538c58061d44f849b1a1102e6b , which didn't actually change anything in the msd code

#4 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2604.
Uploader: Roland Schulz ()
Change-Id: gromacs~master~Ie0f1bb881d8ba1b5cc363c3645130123245c98a6
Gerrit URL: https://gerrit.gromacs.org/8170

#5 Updated by Roland Schulz over 1 year ago

  • Status changed from New to Resolved

#6 Updated by Paul Bauer over 1 year ago

  • Status changed from Resolved to Closed

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