Hi guys,
I've got a new setup for computing bonded interactions in pmemd. It
improves the throughput somewhat (though I must admit the calculation is
surprisingly arithmetic bound). It also affords an interesting opportunity
to push the envelope of what Amber can do, and I think it would patch a
vulnerability we've got right now.
WHAT I COULD DO:
Permit systems with molecules whose bonded structure wraps in a periodic
simulation box. You could do a continuous graphene sheet, a MOF crystal,
continuous cellulose fibers. This would all be accomplished by locally
re-imaging the groups of atoms taken in by each bond work unit.
I THINK IT'S A BUG FIX:
The current setup re-images all coordinates, molecule by molecule, relative
to a single reference frame, then applies the NMR restraints (and any
bonded interactions) to those coordinates. Bonds are safe, but if an NMR
restraint applies between two separate molecules, there is a slim chance
that they will have been re-imaged in a way that suddenly puts an
additional box length between them. So the proposed change, which would
locally re-image coordinates with respect to the interactions at hand,
would stand a much lower chance of doing that. (There's still an edge case
where the code makes a work unit out of a series of NMR restraints that are
somehow chained together in a way that spans the box, meaning that no
single re-imaging of even the local group of coordinates is valid.)
I'm floating this just in case anyone has experience or knows something
about how NMR restraints are intended to function that I haven't foreseen.
Please feel free to chime in or drop me a PM.
Dave
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Received on Wed Nov 08 2017 - 12:00:02 PST
