[gmx-developers] Re: free energy calculations with restraints

David Mobley dmobley at gmail.com
Fri Jun 21 22:44:25 CEST 2013


Anyone have any insights on this? Do we need to think about implementing
angle/torsional restraints in the pull code, or can we re-cast the
restraints available within topology files to use absolute atom numbering?


On Fri, Jun 14, 2013 at 12:47 PM, David Mobley <dmobley at gmail.com> wrote:

> 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
> questions:
> 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'?
> Thanks!
> David
> --
> David Mobley
> dmobley at gmail.com
> 949-385-2436

David Mobley
dmobley at gmail.com
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