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Bug #2815

gmx msd -mol broken

Added by David van der Spoel 4 months ago. Updated 4 months ago.

Status:
Closed
Priority:
Normal
Assignee:
David van der Spoel
Category:
analysis tools
Target version:
2020
Affected version - extra info:
Master
Affected version:
2020
Difficulty:
uncategorized
Close

Description

In a simplification of gmx msd a bug was introduced such that the -mol flag does not work anymore. See https://gerrit.gromacs.org/#/c/8789/

Associated revisions

Revision 52b48193 (diff)
Added by David van der Spoel 4 months ago

Revert "Removed t_topology from gmx msd"

This reverts commit b9e0922af7eccbb4b9110dd0ea99cdac0244a27a.

See #2815

Change-Id: Ie0ae90febf1e170b2c1743ef63b36a567fdabff4

Revision 57b3bfe3 (diff)
Added by David van der Spoel 3 months ago

MSD tests for the -mol option.

Had to free some memory as well to make tests pass.
Added basic code for running grompp.

Renamed spc5 files in simulationdatabase that are used
in src/programs/mdrun/tests to tip3p5 since they were
in fact using tip3p and in this manner a conflict with
the gmx_msd tests is avoided.

TODO: re-use the grompp code in moduletest.cpp
from src/programs/mdrun/tests

Part of #2815

Change-Id: I5d5d33f431f1d3089ebaef54b6388348d47ce6e2

History

#1 Updated by Gerrit Code Review Bot 4 months ago

Gerrit received a related patchset '2' for Issue #2815.
Uploader: David van der Spoel ()
Change-Id: gromacs~master~Ie0ae90febf1e170b2c1743ef63b36a567fdabff4
Gerrit URL: https://gerrit.gromacs.org/8873

#2 Updated by Gerrit Code Review Bot 4 months ago

Gerrit received a related patchset '1' for Issue #2815.
Uploader: David van der Spoel ()
Change-Id: gromacs~master~I5d5d33f431f1d3089ebaef54b6388348d47ce6e2
Gerrit URL: https://gerrit.gromacs.org/8875

#3 Updated by David van der Spoel 4 months ago

Code has been reverted.

#4 Updated by David van der Spoel 4 months ago

  • Status changed from New to Closed

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