center of mass motion removal with position restraints can lead to artifacts
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.
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.
#2 Updated by Erik Lindahl about 2 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...