Re: Fwd: Re : Setting up a membrane simulation

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Sep 20 2011 - 05:43:30 CDT

Google will help you to find literature on this topic and what ensemble they
used.
Ask yourself:
Under which ensemble would you run the experiment in a lab ;-)

Cheers,
Bjoern

On Tuesday 20 September 2011 12:04:15 kanchi subbarao rao wrote:
> thanking to you BJoern,
> I am using charmm36 FF and I built bilayer in charmm-gui. I am
> trying to see bilayer melting.
> please Let me clarify In this case is the NPgT ensemble is need
> or not.
> can you suggest me which ensemble(among NPT, NPAT, or NPgT) is
> apt.
>
>
>
> regards
> subbarao kanchi.
>
> On Tue, Sep 20, 2011 at 2:57 PM, Bjoern Olausson
<namdlist_at_googlemail.com>wrote:
> > 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

-- 
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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