Re: Fwd: Re : Setting up a membrane simulation

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Sep 20 2011 - 04:27:23 CDT

On Monday 19 September 2011 19:25:47 kanchi subbarao rao wrote:
> hi Bjoern,
>
> Its so nice.the suggestions which are given by you , are
> really valuable for all of us.But I need small clarification,
> 1. Are the constraints require while in initial minimization step?
>
You might want to make yourself familiar what happens during the minimization
run (minimize). This will answer your question ;-)

> 2. how to bring area per lipid to desired (experimental) while
> equilibration, is any stander protocol for this?
>
Well, you have to place them accordingly during the setup and keep them in
this place while equilibrating.

> 3. If we use constant area (NPAT) , how can we measure area per lipid
> or area per head as function of temperature?
>
Maybe I misunderstand your question.
But to get the projected area per lipid, you just divide the unit cell
dimensions X*Y by half the number of lipids (assuming your membrane is bilayer
and aligned to the membrane normal Z).
I must admit that I never calculated Lipids/Area since I do rely on the order
parameter as indicator for a reasonable membrane setup.

> 4. when the simulations in NPgT ensemble are needed (significant )
> in our bilayer simulations
>
How can I tell? I don't even know which FF you are using, nor do i know what
you do want to calculate from you simulation.
Surface Tension Target (STT) introduces a surface tension in the X-Y plane to
compress or decompress the lipids in this area. The right amount of pressure
should yield proper Area/Lipid distribution and order parameters. If you
choose to go with NPgT make sure you crunch enough time (80 to 100ns) to reach
equilibration. You might want to run two or three simulations parallel to
estimate the target STT which then should yield your prober observable
(whatever parameter from experimental results).

Cheers,
Bjoern

-- 
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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