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Bug #2219

Orientation restraint reference issue

Added by Berk Hess over 2 years ago. Updated over 2 years ago.

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

For fitting the molecule to the reference structure for applying orientation restraints, the current structure was shifted by the center of mass of the reference structure instead of the current structure. Obviously, if the molecule doesn't drift much during the simulation, this has little effect. If it moves a lot, the restraining is still correct (unless ensemble averaging is used). The only incorrect output is the orientation of the molecule.
This bug seems to have been present since the first version of the code.

Associated revisions

Revision 74391574 (diff)
Added by Berk Hess over 2 years ago

Fix orientation restraint reference

The resetting of the COM of the molecule with orientation restraints
for fitting to the reference structure was done with the COM of the
reference structure instead of the instantaneous structure. This does
not affect the restraining (unless ensemble averaging is used), only
the printed orientation tensor.

Fixes #2219.

Change-Id: I4984ee7f64780a5c3850feb4bfe4a624afd5cec7

Revision 3e3c2ea0 (diff)
Added by Berk Hess over 2 years ago

Fix orientation restraint reference

The resetting of the COM of the molecule with orientation restraints
for fitting to the reference structure was done with the COM of the
reference structure instead of the instantaneous structure. This does
not affect the restraining (unless ensemble averaging is used), only
the printed orientation tensor.

Fixes #2219.

Change-Id: I4984ee7f64780a5c3850feb4bfe4a624afd5cec7

History

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

Gerrit received a related patchset '1' for Issue #2219.
Uploader: Berk Hess ()
Change-Id: gromacs~master~I4984ee7f64780a5c3850feb4bfe4a624afd5cec7
Gerrit URL: https://gerrit.gromacs.org/6811

#2 Updated by Berk Hess over 2 years ago

  • Status changed from In Progress to Fix uploaded

#3 Updated by Berk Hess over 2 years ago

  • Status changed from Fix uploaded to Resolved

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

Gerrit received a related patchset '1' for Issue #2219.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2016~I4984ee7f64780a5c3850feb4bfe4a624afd5cec7
Gerrit URL: https://gerrit.gromacs.org/6821

#5 Updated by Mark Abraham over 2 years ago

  • Target version changed from 2018 to 2016.4

#6 Updated by Mark Abraham over 2 years ago

  • Status changed from Resolved to Closed

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