[gmx-developers] free energy calculations with restraints

David Mobley dmobley at gmail.com
Fri Jun 14 21:47:13 CEST 2013

Hi, devs,

I'm writing with an issue relating to the interplay of new free energy
features with restraints.

I'm very much appreciating some of the new free energy features in gromacs,
such as the 'couple-moltype' option which provides a way to set up
decoupling or annihilation of a specific molecule via free energy
calculations without having to edit the topology file directly. This is
especially great when it comes to decoupling -- charge decoupling was not
previously possible via topology file editing, and vdW decoupling took
substantial manipulation of the topology file.

However, for binding free energies, my work employs orientational
restraints between the protein and ligand. I need to be able to impose both
dihedral and angle restraints on angles between the protein and ligand.
Currently, I do this using angle-restraints and dihedral-restraints. This
requires that both the protein and ligand be within the same logical
'molecule', which (unfortunately) means that I can't make use of the new
free energy features above, since couple-moltype has to apply to a whole
molecule, not just part of a molecule.

So, my I see two possible solutions to the problem, and hence have these
1) Can dihedral and angle restraints be applied via the pull code? If not,
are there any plans to add that?
2) Alternatively, what about modifying the restraints code so it uses (or
at least optionally allows) absolute atom numbering, rather than numbering
within a specific molecule, thus allowing restraints (angle-restraints and
dihedral-restraints) to be applied between 'molecules'?


David Mobley
dmobley at gmail.com
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