Self-Assemble Monolayer--Periodic Boundary Conditions

From: Natnael Doilicho (
Date: Mon Sep 29 2014 - 18:03:18 CDT

Hi all,

I am simulating an Alkanethiol Self-Assembled Mononlayer.

The layer has at its base a hexagonally patterned plane of Sulfur atoms,
each 5 Angstroms from one another.

When I run the equilibration (under NPT conditions), the adjacent image
cells move closer to the original, disturbing the 5 Angstrom exclusion
distance between the sulfur atoms around the edges of the square system.

Is there a way to limit or cease this universal contraction?


Natnael Doilicho
University of Chicago

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