[gmx-developers] free energy calculations with restraints

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Tue Aug 20 17:27:14 CEST 2013

> The pull code is more general in the sense that it can work not only on
> atoms, but also on COMs.
> But the normal bonded code currently supports a lot more potential types

One possibility is to allow the pull code to access bonded functions.

> and will be more efficient, especially in parallel, since it doesn't
> require extra, global communication for restraining ligands.

This is a good point that I was not aware of.  What is the overhead here?

> We are also planning to clean up and generalize the pull code setup by
> separating the pull groups from the distances and the reaction
> coordinates. That would also make it easier to add angle potentials. But
> I don't know what kind of potentials are required for restraining ligands.

Harmonic restraints in bonds / angles / torsions.  Fairly vanilla stuff.

One thing I didn't quite understand is "The only disadvantage is that the
ligand will not automatically end up in the same periodic image as the
protein."  What are the consequences of this?

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

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