AW: Self-Assemble Monolayer--Periodic Boundary Conditions

From: Norman Geist (
Date: Tue Sep 30 2014 - 01:38:57 CDT

So you want to keep cell size in X and Y and only want to adapt pressure in Z?


useflexiblecell yes

useconstantarea yes


Otherwise please explain more general.


Norman Geist.


Von: [] Im Auftrag von Natnael Doilicho
Gesendet: Dienstag, 30. September 2014 01:03
Betreff: namd-l: Self-Assemble Monolayer--Periodic Boundary Conditions


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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