[gmx-developers] free energy calculations with restraints

[David Mobley]

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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-- 
David Mobley
dmobley at gmail.com
949-385-2436
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