[gmx-developers] Brainstorming ideas for minimally painless incorporation of an MC barostat (later MC moves in general)

Shirts, Michael R. (mrs5pt) mrs5pt at eservices.virginia.edu
Thu Jul 17 18:20:43 CEST 2014

Yes: periodic molecules

I think this is mostly solved by coupled constraint system COM constraints (I may be wrong), unless the entire periodic molecule is constrained, which seems like an unlikely case to be running MD on.

> and COM (pull) constraints.

To avoid communication, scaling would need to preserve the distance between these atoms.  Although the distance between the two is known by all nodes (it's a constant), the direction between the constraints is not known, so one wouldn't know where the center of that constrained system was -- so I guess communication would be required in this case.

But maybe I'm totally off, and if a constraint system is split between multiple nodes nodes, there is no easy way to compute the COM of that constraint w/o communication, and one wouldhave to communicate anyway.

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

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