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Bug #3244

center of mass motion removal with position restraints can lead to artifacts

Added by Berk Hess 7 months ago. Updated 7 months ago.

Status:
In Progress
Priority:
Normal
Assignee:
Category:
-
Target version:
Affected version - extra info:
all prior versions
Affected version:
Difficulty:
uncategorized
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Description

When position restraints are present, the system has an absolute references in space and then center of mass motion is often not needed and might even cause artifacts.
I think we should automatically turn off center of mass motion for such cases (along dimensions which have position restraints). But this will affect many standard run protocols which start with position restraining and have COM removal on by default.
For now I will suggest adding a warning in grompp. This should probably only be a note, as otherwise many workflows will break.

Associated revisions

Revision c900b356 (diff)
Added by Berk Hess 7 months ago

Add note for COM removal with position restraints

Center of mass motion removal in combination with position restraints
will often cause artifacts. We should (automatically) disable this,
but this will disrupt workflows, so for now grompp will issue a note.

Refs #3244

Change-Id: If983e918d26f0af2fab96d44d0f2b1fc3cedb901

History

#1 Updated by Artem Zhmurov 7 months ago

  • Target version changed from 2020 to 2021

#2 Updated by Erik Lindahl 7 months ago

I don't think it's a good idea to do something else than the user asked for under-the-hood - that seems like asking for a future bug report when something goes horribly wrong.

Having a warning sounds like a good idea, though. If people rely on this in their existing workflows I would even argue it's a good idea to "break" them and notify the users they are relying on something that's bad practice?

Maybe we should make it a note for now since it's so late in the beta cycle...

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