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Bug #2703

constraint and mass contributions missing from foreign Hamiltonian values

Added by Berk Hess about 1 year ago. Updated 10 months ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
all versions
Affected version:
Difficulty:
uncategorized
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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 about 1 year 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 about 1 year 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 10 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 10 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 about 1 year 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 about 1 year ago

Reasonable also to fix in release-2016

#3 Updated by Gerrit Code Review Bot about 1 year 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 about 1 year 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 about 1 year ago

  • Status changed from Fix uploaded to Closed

#6 Updated by Mark Abraham 10 months ago

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

#7 Updated by Gerrit Code Review Bot 10 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 10 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 10 months ago

  • Target version changed from 2018.4 to 2018.6

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