[gmx-developers] Re: free energy calculations with restraints

[Shirts, Michael (mrs5pt)]

Looking through very briefly, I would think this should be possible to do
through the pull code.  Basically, you could have an index group with 3 or 4
atoms, which can then be as angles or dihedrals.

Anyone with more expertise with the pull code who can comment further as to
whether this would work?
 
Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: David Mobley <dmobley at gmail.com>
> Date: Fri, 21 Jun 2013 13:44:25 -0700
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Cc: "Michael R. Shirts" <michael.shirts at virginia.edu>
> Subject: Re: free energy calculations with restraints
> 
> 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