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Bug #2703

constraint and mass contributions missing from foreign Hamiltonian values

Added by Berk Hess 11 months ago. Updated 7 months ago.

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

Description

The foreign Hamiltonian values only contain the potential energy terms. The constraint and kinetic energy contributions are missing.


Related issues

Related to GROMACS - Bug #2849: Free energy discrepancies between GROMACS versionsClosed

Associated revisions

Revision 1d8678d9 (diff)
Added by Berk Hess 11 months ago

Add missing constraint term to deltaH

The constraint contribution was missing from foreign Hamiltonian
difference output from mdrun used for BAR.

Refs #2703

Change-Id: I00fb88bed76f9ff03faed7543e90adf163b99f08

Revision b51dbae2 (diff)
Added by Berk Hess 11 months ago

Add missing mass term to deltaH

The mass contribution was missing from foreign Hamiltonian difference
output from mdrun used for BAR.

Refs #2703

Change-Id: I415c835e9e1a8473243041be004013af7141a1cc

Revision a741d07b (diff)
Added by Berk Hess 7 months ago

Fix mass Delta H double counting

With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.

Refs #2703
Fixes #2849

Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c

Revision 499ab90c (diff)
Added by Berk Hess 7 months ago

Fix mass Delta H double counting

With separate mass lambda parameters, the perturbed mass contribution
to Delta H (not dH/dlambda) was double counted. This was due to an
incorrect fix for issue #2703 for missing Delta H contribution.

Refs #2703
Fixes #2849

Change-Id: I1349260e1e90a17a6b7dbe0d239d9474dcfa928c

History

#1 Updated by Gerrit Code Review Bot 11 months ago

Gerrit received a related patchset '1' for Issue #2703.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I00fb88bed76f9ff03faed7543e90adf163b99f08
Gerrit URL: https://gerrit.gromacs.org/8569

#2 Updated by Mark Abraham 11 months ago

Reasonable also to fix in release-2016

#3 Updated by Gerrit Code Review Bot 11 months ago

Gerrit received a related patchset '1' for Issue #2703.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I415c835e9e1a8473243041be004013af7141a1cc
Gerrit URL: https://gerrit.gromacs.org/8570

#4 Updated by Berk Hess 11 months ago

  • Subject changed from constraint contribution missing from foreign Hamiltonian values to constraint and mass contributions missing from foreign Hamiltonian values
  • Status changed from In Progress to Fix uploaded

#5 Updated by Paul Bauer 11 months ago

  • Status changed from Fix uploaded to Closed

#6 Updated by Mark Abraham 8 months ago

  • Related to Bug #2849: Free energy discrepancies between GROMACS versions added

#7 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '1' for Issue #2703.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2019~I1349260e1e90a17a6b7dbe0d239d9474dcfa928c
Gerrit URL: https://gerrit.gromacs.org/9141

#8 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '1' for Issue #2703.
Uploader: Berk Hess ()
Change-Id: gromacs~release-2018~I1349260e1e90a17a6b7dbe0d239d9474dcfa928c
Gerrit URL: https://gerrit.gromacs.org/9172

#9 Updated by Paul Bauer 7 months ago

  • Target version changed from 2018.4 to 2018.6

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