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Bug #2720

Normal-mode analysis with vsites or shells works for first molecule of each type only

Added by David van der Spoel 6 months ago. Updated 5 months ago.

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

Description

The routine get_atom_index in mtop_util.cpp works for only one molecule at a time. The routine is used for normal mode analysis with vsites or shells and for analysis of the result using gmx nmeig.


Related issues

Has duplicate GROMACS - Bug #2721: get_atom_index does not work with multiple moleculesClosed

Associated revisions

Revision e9b526ba (diff)
Added by David van der Spoel 6 months ago

Updated normal modes output for sw-dimer.

Due to a bug in mtop_util.cpp only the first molecule in the
sw-dimer was used in a normal mode analysis. This is fixed in patch
https://gerrit.gromacs.org/#/c/8631/.

Fixed a bug in gmxtest.pl when comparing two xvg files where the
reference value is zero (it computed the relative difference and
divided by zero). This only showed up in the new output file
normal_modes/sw_dimer/eigenfreq.xvg.

Part of #2720

Change-Id: Iae990bbff2c19c28310618f2cadf1157a62242d0

Revision 4dede5be (diff)
Added by David van der Spoel 6 months ago

Change get_atom_index to allow multiple molecules.

Make gromacs take into account atoms in all molecules.
This allows Hessian matrix creation to work over all
molecules in a simulation. An update to the regression
tests has been submitted as well.

During fixing of the problem, another problem surfaced in
the normal mode calculations to do with ordering of atoms
which is fixed here as well.

Fixes #2720

Change-Id: I9fc2dd05cb1c67d46b6d4c3d9139e6b3bed72f17

History

#1 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '3' for Issue #2720.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2019~I153b9a29ba4cd602d77d4ab529ab4e97c68fa264
Gerrit URL: https://gerrit.gromacs.org/8624

#2 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '1' for Issue #2720.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2018~I153b9a29ba4cd602d77d4ab529ab4e97c68fa264
Gerrit URL: https://gerrit.gromacs.org/8629

#3 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '1' for Issue #2720.
Uploader: David van der Spoel ()
Change-Id: regressiontests~release-2018~Iae990bbff2c19c28310618f2cadf1157a62242d0
Gerrit URL: https://gerrit.gromacs.org/8630

#4 Updated by Gerrit Code Review Bot 6 months ago

Gerrit received a related patchset '1' for Issue #2720.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2018~I9fc2dd05cb1c67d46b6d4c3d9139e6b3bed72f17
Gerrit URL: https://gerrit.gromacs.org/8631

#5 Updated by Mark Abraham 6 months ago

  • Has duplicate Bug #2721: get_atom_index does not work with multiple molecules added

#6 Updated by Mark Abraham 6 months ago

  • Subject changed from Routine get_atom_index works for one molecule only to Normal-mode analysis with vsites or shells works for one molecule only

#7 Updated by David van der Spoel 6 months ago

  • Subject changed from Normal-mode analysis with vsites or shells works for one molecule only to Normal-mode analysis with vsites or shells works for first molecule of each type only

#8 Updated by David van der Spoel 6 months ago

A problem with the normal mode calculations itself surfaced as well unfortunately, related to virtual sites and shells.

#9 Updated by David van der Spoel 6 months ago

  • Status changed from New to Resolved

#10 Updated by Paul Bauer 5 months ago

  • Status changed from Resolved to Closed

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