Re: [AMBER] Bias Towards the Periodic Boundary

From: Timothy Schutt <>
Date: Wed, 18 Oct 2017 15:11:43 -0500

Thanks for the input! I used VMD to shift/re-image the periodic box and am
running the shifted big system longer under the same conditions (...well
waiting in queue to run).

I also created a much smaller system (2 ions, 500 waters, 37A box length)
and am running it on my local desktop to try and get results faster on just
the boundary preference possibility since the big system takes a long time
to run and our HPC has long queues.

The small systems are running locally - one under the same conditions to
verify the same phenomenon with a smaller system, and another under NVE,
iwrap=0, and using Sander.mpi, to check if those have the potential to
change it. Depending on these results I'll put together a bunch of replicas
to get statistics and or individually change parameters... I'll keep you
guys posted!


On Wed, Oct 18, 2017 at 3:03 PM, David A Case <>

> On Wed, Oct 18, 2017, Timothy Schutt wrote:
> >
> > I've long suspected that there was some small artificial spatial bias
> > towards the periodic boundaries because my macromolecules would always
> > migrate towards the vertices and then stay there but I never really
> > investigated it because I thought it would Not impact my dynamics results
> > at all. However, I recently tried to simulate a droplet and the artifact
> is
> > even more readily apparent.
> I think the bias is unlikely, but it's good that people test these things.
> I'd definitely recommend running with iwrap=0: use cpptraj to do any
> necessary
> imaging. cpptraj also has the "replicatecell" action, which can help in
> visualization (or you can generate multiple unit cells in visualization
> programs like VMD or Chimera).
> >
> > 1. Have other people observed this behavior; is it a known artifact?
> > I wasn't able to find any documentation on it in this forum or general
> web
> > search.
> >
> > I'm using amber16 pmemd.MPI. My system is mostly aqueous (TIP4PEW) and
> the
> > box dimensions are much larger than they need to be. I expected most of
> the
> > molecules to coalesce into a somewhat spherical shape on their own during
> > NVT equilibration due to minimizing surface area to volume ratio as the
> > force field should encourage naturally... and then much of the simulation
> > box should be empty or have a few 'volatile' compounds floating around.
> > Instead, however, the liquid lined up along the 4 parallel vertices, in
> > essence forming an infinitely long column centered on the corners between
> > periodic images. Therefore I believe the amount of bias at the boundary
> has
> > a net effect on the same order of magnitude as water's surface tension!
> I'm not sure I follow what you are saying here (about "4 parallel
> vertices").
> But it's sounds possible that an "infinitely long column" would indeed
> minimize the surface area per molecule, since you would have water-water
> contacts between cells, which would be more favorable than water-air
> contacts.
> If so, this would be a "feature" of periodically replicated systems, rather
> and a bug or bias in the code.
> ....dac
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Received on Wed Oct 18 2017 - 13:30:04 PDT
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