GROMACS

I first mailed Maarten Wolf, who is the author of g_membed,
that a proper API would solve this issue.
But thinking more about it, I realized that g_membed is not a new tool,
but rather a small extension of mdrun.
Therefore I would suggest an extra input file to mdrun, similar in spirit
to the old pull code implementation, to pass the extra parameters
to some extra functions in mdrun.

PS I assigned the bug to Gerrit, since Maarten does not have a bugzilla account.

Berk

Moved g_membed functionality to mdrun

I saw you committed this only in git master and not in the 4.5 release.
I don't know if we would want that or not.
(don't do it right away, because we might have merge conflicts.)

Berk

Let's not add this in release-4-5 patches; there's nothing wrong with the code, so let's restrict that branch to bugfixes!