AW: Self-Assemble Monolayer--Periodic Boundary Conditions

From: Norman Geist (norman.geist_at_uni-greifswald.de)
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: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Natnael Doilicho
Gesendet: Dienstag, 30. September 2014 01:03
An: namd-l_at_ks.uiuc.edu
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?

 

Thanks,

Natnael Doilicho

University of Chicago

 

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