[gmx-developers] free energy calculations with restraints

[Erik Marklund]

Yes I do. I'm currently revising the manuscript that prompted this implementation to begin with. After that I will probably port it into a release branch if other developers think it's a good idea. Just to be clear: it's not ordinary distance/angle restraints, but a tweak to the pull code to make use of helical and circular reaction coordinates.

Erik

On 1 Jul 2013, at 22:48, David Mobley <dmobley at gmail.com> wrote:

> Thanks. Do you have any interest in doing so?
> 
> Also, to the developers more broadly: I believe the current code also doesn't support lambda exchange with multiple cores per lambda value when using distance restraints (via 'distance_restraints' in the topology file) which is probably another argument towards trying to make the restraints functionality in the pull code work better to replace the restraints functionality currently in topology files, as right now I have several different things I'd like to do that just can't be done without code changes.
> 
> Thanks!
> 
> 
> On Sun, Jun 30, 2013 at 2:01 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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
>>> -- 
>>> 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.
>> 
>> 
>> --
>> 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.
>> 
>> 
>> 
>> -- 
>> 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.
> 
> 
> --
> 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.
> 
> 
> 
> -- 
> 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/20130701/a6508bb1/attachment.html>