membed is apparently broken
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.
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.
#2 Updated by Gerrit Groenhof about 4 years ago
- File conf.gro conf.gro added
- File grompp.mdp grompp.mdp added
- File topol.top topol.top added
- File hex.itp hex.itp added
- File membed.dat membed.dat added
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
gmx mdrun -membed