Re: [AMBER] Bias Towards the Periodic Boundary

From: David A Case <>
Date: Wed, 18 Oct 2017 16:03:02 -0400

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.


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Received on Wed Oct 18 2017 - 13:30:03 PDT
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