make an end to end test for membed - Redmine #2947

When using the membed functionality in mdrun, a segfault occurs after selecting the relevant groups.
The issue seems to be present since at least the original 2019 release and is still present at release-2019^HEAD.

Commands to reproduce

gmx mdrun -nt 1 -s gmembed.tpr -membed gmembed.dat -c pi_pH70_popc_further_solvate.pdb -mn index_before_gmembed.ndx -v

select group 1 for protein
select group 13 for POPC

(from redmine: issue id 2947, created on 2019-05-09 by acmnpv)

• Changesets:
  • Revision 63b3d45c by Paul Bauer on 2019-05-24T13:03:57Z:

Fix membrane embedding

Refactoring forgot to allocate some data, causing a segmentation fault.
More refactoring used wrong data, causing a crash further on.
Even more refactoring lead to invalid memory access.

Fixes #2947

Change-Id: I61ad3125102b50c0338e0935a75cd7b1de95bc3f

• Uploads:
  • index_before_gmembed.ndx
  • gmembed.tpr
  • gmembed.dat