Re: NVT setup for monolayer

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Apr 13 2011 - 10:09:49 CDT

I don't recall those options having any effect for constant volume or on
the pressure calculation.

-Jim

On Thu, 7 Apr 2011, Bjoern Olausson wrote:

> 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:
>
> useGroupPressure
> useFlexibleCell
> useConstantArea
> useConstantRatio
>
> 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
>
> --
> 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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