[gmx-developers] free energy calculations with restraints

David Mobley dmobley at gmail.com
Fri Aug 16 18:30:45 CEST 2013

This does sound useful, though it would be more useful if this could be
implemented into the main GROMACS rather than a separate code (since
otherwise it will go away as GROMACS is further developed).

Would this be a possibility going forward, devels?


On Fri, Aug 16, 2013 at 3:07 AM, Floris Buelens <floris_buelens at yahoo.com>wrote:

> Hi David,
> I have the same requirement as you, but I've gone about it slightly
> differently. I've hacked the couple-moltype code path to allow decoupling
> of a specific residue (identified by name) instead of a molecule. This
> allows the residue of interest to be part of another molecule block so you
> can set up distance, angle and dihedral restraints using regular bonded
> interactions with full perturbation support.
> If this is useful to you or to anyone else, let me know and I'll be happy
> to share.
> best,
> Floris
> ________________________________
> From: David Mobley <dmobley at gmail.com>
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Sent: Friday, 14 June 2013, 21:47
> Subject: [gmx-developers] free energy calculations with restraints
> 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
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David Mobley
dmobley at gmail.com
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