[gmx-developers] free energy calculations with restraints

[Erik Marklund]

It's my personal copy. Also it was based on 4.5.5, but I would think that my changes should be fairly easy to port to 4.6.X.

Erik

On 29 Jun 2013, at 19:39, David Mobley <dmobley at gmail.com> wrote:

> Erik,
> 
> That's good to know. By "hacked", do you mean this is in your personal copy, or is it in the release?
> 
> Thanks.
> 
> 
> 
> On Mon, Jun 24, 2013 at 2:28 AM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> Hi,
> 
> I hacked the pull code to work in the direction of a helical reaction coordinate. In the special case of helix pitch == 0 you get angular or torsional restraints. It could probably do with further generalisation, but at least it's a starting point if anyone's interested.
> 
> Erik
> 
> On 21 Jun 2013, at 22:44, David Mobley <dmobley at gmail.com> wrote:
> 
>> Hi,
>> 
>> 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?
>> 
>> Thanks.
>> 
>> 
>> 
>> 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
>> 949-385-2436
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