[gmx-developers] Implementing Ensemble-Averaged Restraint

[Smith, Colin]

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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