[gmx-users] conveniently placing restraints on a subset of a molecule

[Miro Astore]

Hello,

I am new to the gromacs work flow, I come from using NAMD.

An example of what I want to do is place harmonic restraints on a subset of
a molecule, for example all of the CA atoms in a protein backbone. I have
found the genrestr function which I would have expected would do the trick.

However, as stated in the documentation the indexes won't reflect those
within the molecule. I'm wondering if there is a simple way to do what I
want using the gromacs work flow that doesn't include manually editing the
itp files.

Best, Miro.