Re: NVT setup for monolayer

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Thu Apr 14 2011 - 02:17:35 CDT

Thanks a lot for sharing your experience.

Cheers,
Bjoern

On Wednesday 13 April 2011 17:09:49 Jim Phillips wrote:
> 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
> >
> >
> > Phone: +49-345-55-24942

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

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