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Bug #2228

PBC issue with orientation restraints and the Verlet scheme

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

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
-
Affected version - extra info:
all versions with the Verlet scheme
Affected version:
Difficulty:
uncategorized
Close

Description

With the Verlet cut-off scheme molecules are not whole during the force calculation, whereas this is required for the fitting with orientation restraints. This will cause issues when part of a molecule moves over the boundary of the unit cell. Without time and ensemble averaging this would not affects the potential and forces, only the eigenvectors printed in the log file.
Note that this in practice this likely did not cause issues, since orientation restraints do not work correctly with OpenMP, which is used by default with the Verlet cut-off scheme.

Associated revisions

Revision 899b4c2e (diff)
Added by Berk Hess over 2 years ago

Use graph with orientation restraints

With the Verlet cut-off scheme by default molecules are not made whole.
Now they are made whole when orientation restraints are used.
Added checks and assertions for correct PBC treatment with orientation
restraints.

Fixes #2228.

Change-Id: Ib33294cb9b0b0d131b0c385c001b7cb73c006ba9

History

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

Gerrit received a related patchset '3' for Issue #2228.
Uploader: Berk Hess ()
Change-Id: gromacs~master~Ib33294cb9b0b0d131b0c385c001b7cb73c006ba9
Gerrit URL: https://gerrit.gromacs.org/6836

#2 Updated by Berk Hess over 2 years ago

  • Status changed from Fix uploaded to Resolved

#3 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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