[gmx-developers] gromacs.org_gmx-developers Digest, Vol 178, Issue 4

[Peter Kasson]

Hi Colin,
  The fully implemented, documented API is indeed for pairs of atoms.
There is ongoing work, in part complementary to Christian Blau's
development, that can handle more generic iForceProviders.  That is a
little farther down our development priority list.  However, I suggest you
chat with Christian if you want to implement something for a specific use
case.

David--I think you also had a question about this code path.  The point of
generality in ongoing external force development really is the
iForceProvider work (c.f. Christian and others), and that's probably the
best place to hook in.  I don't think it's a problem at this point if
Gromacs has different interfaces for using iForceProvider code for external
interactions.

Best,
--Peter

----------------------------------------------------------------------
Peter Kasson, MD, PhD
Associate Professor
Departments of Molecular Physiology and Biological Physics
and of Biomedical Engineering
University of Virginia


On Wed, Feb 6, 2019 at 3:01 AM <
gromacs.org_gmx-developers-request at maillist.sys.kth.se> wrote:

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>    1. Re: Implementing Ensemble-Averaged Restraint (Smith, Colin)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Tue, 5 Feb 2019 14:27:47 +0000
> From: "Smith, Colin" <colin.smith at wesleyan.edu>
> To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] Implementing Ensemble-Averaged Restraint
> Message-ID: <0F1E5C79-C0D3-41B9-9BF4-5BB07354EA1F at wesleyan.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Peter,
>
> Thanks for the pointer. It seems like this could work, but the forces
> calculated by my restraint do not always decompose into pairs of atoms.
> Some of the forces depend on the positions of up to six hydrogen atoms at
> once.
>
> As far as I can tell, there?s no way through the API as implemented to get
> access the more than two atoms at a time. Perhaps there?s some way to use
> SessionResources to read more coordinates when RestraintPotential::update()
> gets called on the master rank?
>
> Cheers,
>
> Colin
>
> On Feb 2, 2019, at 06:58, Peter Kasson <kasson at virginia.edu<mailto:
> kasson at virginia.edu>> wrote:
>
> Hi Colin,
>       Take a look at the custom force plugins.  These may not be efficient
> for most of the hydrogens on a large protein (they were designed for
> relatively sparse restraints), but they should at least get you started.
>
> API for doing this:  https://doi.org/10.1093/bioinformatics/bty484
> Application to ensemble-averaged restraints for DEER:
> https://doi.org/10.1002/anie.201810462
>
> Best,
> --Peter
>
> ----------------------------------------------------------------------
> Peter Kasson, MD, PhD
> Associate Professor
> Departments of Molecular Physiology and Biological Physics
> and of Biomedical Engineering
> University of Virginia
>
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