Incorrect COM velocity correction with frozen atoms
The mass for COM removal groups includes the masses of frozen atoms, when present. This leads to a too small velocity correction for the non-frozen atoms.
Frozen atom (dimensions) should not contribute to the COM mass.
Relates to #2551
Remove frozen atoms from VCM groups
Atoms are removed during preprocessing.
Also add release note missing for previous patch.
Fix center of mass motion removal with frozen atoms
When frozen atoms were part of center of mass motion removal groups,
they would still contribute to the mass of those groups. This meant
that the COM velocity correction was (slightly) too small. Now
completely frozen atoms are removed from COM removal groups by grompp.
When atoms are only frozen along one or two dimensions and part of
a COM removal group, grompp now issues a warning.
Also fixed an nullptr or incorrect string buffer passed to warning()
with invalid freeze group dimension user input.
#5 Updated by Berk Hess about 1 month ago
- Status changed from Closed to In Progress
The current fix merged into release-2020 is incorrect as it removes atoms frozen only along one or two dimensions from the VCM group.
Fully frozen atoms can be removed.
Atoms frozen along only one or two dimensions would need to be removed only along the frozen dimensions, but our code does not support this. The simplest solution is to not remove such atoms and issue a warning (not a note).