[AMBER] Bias Towards the Periodic Boundary

From: Timothy Schutt <tschutt7.gmail.com>
Date: Wed, 18 Oct 2017 12:37:56 -0500

Hi All,

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.

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

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!

2. Is this an artifact of the PBC iwrap algorithm somehow... Or perhaps
does the langevin thermostat interact preferentially with molecules at the
edge or something?

My input parameters were:

Test nvt on droplet
 # Control Section

My system is 9000 water molecules with ~60 solute molecules in a box that
is 100A x 100A x 100A (roughly 80% void space). I'm looking at the
aggregation and association of small solutes (both charged and not) in
water droplets and the preference to reside at the surface of the droplet.
I think this PBC bias would impact my results this time.

3. Is there a known fix?

If not, I'll try running without iwrap, or in sander, and/or loosening to
NVE constraints to start diagnosing where the bias is coming from but I'm
hoping it's already known.

4. If this isn't already known, any suggestions in where/how to look for
the cause in addition to the above?

Thanks for the help!!

-Timothy Schutt
Vicksburg, MS
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Received on Wed Oct 18 2017 - 11:00:03 PDT
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