Re: [AMBER-Developers] [AMBER] Any issues if I make PMEMD understand bonds span imaging?

From: Josh Berryman <>
Date: Thu, 7 Apr 2016 08:37:56 +0200

Could be handy for DNA, its very convenient to fix the linking number by
making a topologically closed structure, but without having to bend it
around in a circle.

On 6 April 2016 at 22:56, Jason Swails <> wrote:

> Moving this to the dev list where it's more appropriate
> On Wed, Apr 6, 2016 at 4:49 PM, David Cerutti <> wrote:
> > It's been asked before, but I've been contemplating my next career moves
> > and a number of problems in materials science would be a lot easier to do
> > with Amber if it could simulate systems in which bonded structures could
> > extend infinitely. Having implemented the functionality in mdgx, I would
> > say that, in principle, the only thing that needs to change in PMEMD /
> > sander to have a bond traverse the box imaging would be to import the box
> > dimensions, make appropriate copies of the coordinates, then transform
> and
> > image the copies to compute forces and energies.
> >
> > Any objections if I take this on? Might be something nice to do early
> in a
> > cycle, so there can be lots of testing before the next release. Can
> anyone
> > suggest things I might break if I try this?
> >
> ​collective variable restraints. It may also complicate
> exclusion/exception rules.
> ​Are you going to change the whole bonded routines (bonds, angles, and
> torsions) to use MIC displacements​ instead of raw displacements? Are you
> going to introduce new valence lists that list *just* the terms that will
> span the PBC?
> If there's ever a case where a bond distance becomes large compared to the
> box size (not common with bonds, but *may* be common with collective
> variable restraints), then you start breaking the definition of a "chemical
> bond" (i.e., two specific atoms bonded with each other), since the bond
> definition will jump between an atom and one of its images.
> I've thought about this before... GROMACS also does this, IIRC -- you may
> look at how they handle it for inspiration.
> All the best,
> Jason
> --
> Jason M. Swails
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Received on Thu Apr 07 2016 - 00:00:03 PDT
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