[gmx-developers] free energy calculations with restraints

Floris Buelens floris_buelens at yahoo.com
Fri Aug 16 12:07:37 CEST 2013

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.



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'?


David Mobley
dmobley at gmail.com

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