[gmx-developers] free energy calculations with restraints

[Erik Marklund]

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
> -- 
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20130624/4d3fb30f/attachment.html>