Re: [AMBER-Developers] NMR restraints and re-imaging

From: David A Case <>
Date: Mon, 13 Nov 2017 20:36:29 -0500

On Wed, Nov 08, 2017, Dave Cerutti wrote:
> 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.
> 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.
> 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.

As others have pointed out, this can be a really complex subject, and not
something to be approached in an ad hoc or seat-of-the-pants approach. Here's
my brief take:

1. Simplest (present case, I think): atom ID's for interactions are fixed in
the prmtop file, and don't change. The current coordinates are used, without
checking anything: it's up to the user to ensure that this is what is really
wanted. Pretty secure for covalent interactions that don't break, but doesn't
allow bonds "across" periodic boundaries.

2. Second case, which I think is well-defined, but not implemented: for any
pair of atoms, the minimum image interaction can be unambiguously determined.
(Tricky but doable in non-orthogonal unit cells.) Then an interaction
between two atoms could be marked as "use minimum image here". That would
allow the bonded structure to go across a unit cell boundary. One has to
take care for angles and dihedrals: first: use minimum image to get the
atom-atom vectors involved; then construct the angles/dihedrals out of such
atom-atom vectors. You can probably go back to minimum image for the 1-4
nonbonded terms.

[I *think* this would only work for multi-atom terms that can be constructed
from atom-atom vectors. You can't use this idea for things like
center-of-mass restraints, for example.]

But one would have to make sure that is what is really wanted. I think
it would work for wrapping bonded structures in a periodic simulation
box. It probably won't work for artificial constraints, like NMR distance
constraints that may be broken at times, etc.

Note that "minimum image" is not the same as "imaging" (in the sense that
such a term is used in cpptraj. I think the second ("BUG FIX") idea above,
of reimaging all coordinates and then applying NMR restraints, is unlikely
to work.

...something to think about anyway....dac

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Received on Mon Nov 13 2017 - 18:00:02 PST
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