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

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Sat Jun 22 18:36:12 CEST 2013

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?
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> 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

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