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Bug #1998

membed is apparently broken

Added by Mark Abraham over 3 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Erik told me this is broken, but I have no details, have never used it and plenty of core things still left untested.

This is surely a feature for the post-2016 discussions "ok, who are the maintainers, and what plan can we have for making sure it is tested in an ongoing way?" because if nobody is keen to do the work, then we aren't going to have the feature.

conf.gro (215 KB) conf.gro input structure Gerrit Groenhof, 06/30/2016 05:31 PM
grompp.mdp (11.5 KB) grompp.mdp mdp file Gerrit Groenhof, 06/30/2016 05:31 PM
topol.top (73.5 KB) topol.top topology, needs also hex.itp Gerrit Groenhof, 06/30/2016 05:31 PM
hex.itp (7.26 KB) hex.itp hexane topology Gerrit Groenhof, 06/30/2016 05:31 PM
membed.dat (446 Bytes) membed.dat file with membed options Gerrit Groenhof, 06/30/2016 05:32 PM

Related issues

Related to GROMACS - Task #1971: Removing buggy features vs. keeping workflows New

Associated revisions

Revision 98d6c26b (diff)
Added by Erik Lindahl over 3 years ago

Fix membed with partial revert of 29943f

The membrane embedding algorithm must be initialized before
we call init_forcerec(), so it cannot trivially be moved into
do_md(). This has to be cleaned up anyway for release-2017
since we will remove the group scheme be then, but for now
this fix will allow us have the method working in release-2016.

Fixes #1998.

Change-Id: I8e16a67b8df16999793649d79eebca051b8b474f

History

#1 Updated by Mark Abraham over 3 years ago

  • Related to Task #1971: Removing buggy features vs. keeping workflows added

#2 Updated by Gerrit Groenhof over 3 years ago

Here is an example of embedding an alpha helix into a decane layer. The suppressed warning concerns the energy group exclusions when using PME and can be ignored

gmx grompp -maxwarn 1 << EOF
1
13
EOF
gmx mdrun -membed

#3 Updated by Gerrit Groenhof over 3 years ago

Sorry, mixed up the user-input. I should be

gmx grompp -maxwarn 1
gmx mdrun -membed << EOF
1
13
EOF

#4 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1998.
Uploader: Erik Lindahl ()
Change-Id: I8e16a67b8df16999793649d79eebca051b8b474f
Gerrit URL: https://gerrit.gromacs.org/6029

#5 Updated by Erik Lindahl over 3 years ago

  • Status changed from New to Resolved

#6 Updated by Mark Abraham over 3 years ago

  • Status changed from Resolved to Closed
  • Target version set to 2016

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