NVT setup for monolayer

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Apr 07 2011 - 08:24:32 CDT

Hi NAMD users,

I have setup a symmetrical monolayer
(vacuum (Air) - monolayer - water - monolayer - vacuum (Air))

The membrane is well hung an thus should be in a good equilibrated state.
(Although the leaflet was taken from a bilayer simulation, I think this is
still closer to equilibrium then a fresh build one)

I am wondering how to choose the following Keywords for the NAMD NVT run:


My guess for useGroupPressure:
YES (since I do use shake)

But what about useConstantArea or useConstantRatio

Which one would I prefer?
My guess:
useFlexibleCell YES
useConstantArea NO
useConstantRatio YES

I am not sure if this has an influence on the pressure components since i want
to calculate the surface tension and the surface pressure.

Anny comments or thoughs on this?

Thanks a lot,

Bjoern Olausson
Martin-Luther-Universit├Ąt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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