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Bug #2553

Incorrect COM velocity correction with frozen atoms

Added by Berk Hess almost 2 years ago. Updated about 1 month ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
ant version of gromacs up to 2018
Affected version:
Difficulty:
uncategorized
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Description

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


Related issues

Related to GROMACS - Bug #3406: #DOF for temperature coupling incorrect when some atoms are not part of a COM removal groupClosed

Associated revisions

Revision 3a93c3a8 (diff)
Added by Paul Bauer about 1 month ago

Remove frozen atoms from VCM groups

Atoms are removed during preprocessing.

Also add release note missing for previous patch.

Fixes #2553

Change-Id: I4fd52d50a9ef3af4ed11f9b507902d4ac59ed487

Revision e69b71f3 (diff)
Added by Berk Hess about 1 month ago

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.

Fixes #2553

Change-Id: I20a03fea511e75a131cb27880acc1f4ee4a2bfb8

History

#1 Updated by Berk Hess over 1 year ago

  • Target version changed from 2019 to 2020

The best solution would be that grompp removes frozen atoms from the COM group. We could also instead generate an error when frozen atoms are part of a COM group.

#2 Updated by Paul Bauer 4 months ago

  • Target version changed from 2020 to 2020.1

#3 Updated by Paul Bauer about 1 month ago

  • Status changed from Accepted to Resolved

#4 Updated by Paul Bauer about 1 month ago

  • Status changed from Resolved to Closed

#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).

#6 Updated by Paul Bauer about 1 month ago

I reverted my change

#7 Updated by Paul Bauer about 1 month ago

  • Target version changed from 2020.1 to 2020.2

Nobody else cared about this for a year so it gets bumped instead of being incorrectly fixed

#8 Updated by Berk Hess about 1 month ago

  • Related to Bug #3406: #DOF for temperature coupling incorrect when some atoms are not part of a COM removal group added

#9 Updated by Paul Bauer about 1 month ago

  • Status changed from In Progress to Fix uploaded
  • Target version changed from 2020.2 to 2020.1

Berk has the correct fix now for the 2020.1 patch

#10 Updated by Berk Hess about 1 month ago

  • Status changed from Fix uploaded to Resolved

#11 Updated by Paul Bauer about 1 month ago

  • Status changed from Resolved to Closed

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