Re: Controlling the area per lipid

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Thu Nov 01 2007 - 01:45:31 CDT

Should I just use constant pressure to allow the membrane to shrink. What is
the lateral pressure of a membrane, 1 ATM? What if I just decrease the X
and Y dimensions?

Thanks,

Ilya

On 10/31/07, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>
> Minmax measurements of lipids will not be reliable. Lipids that
> stick out of the simulation cell will still be measured because they
> don't get wrapped until most of the molecule crosses the periodic
> boundary. The water will be more accurate, but the numbers in the
> xst file will be the exact cell size over the simulation. If you are
> using constant area, the x-y numbers should never change.
>
> You should consider during initial equilibration though that the
> membrane may shrink (and may need to), especially if you put a
> protein in the middle and removed all lipids near it. After that,
> you could run constant area though.
>
> On Oct 31, 2007, at 8:23 PM, Ilya Chorny wrote:
>
> > Hi I am having some trouble controlling the area per lipid molecule
> > in my simulation. I set my cell basis vector in the XY plane to the
> > correct area to maintain the proper density but the minmax
> > measurements of my lipid give me values that are larger than the
> > cell basis vectors. I also you constant area pressure coupling.
> > Why is that? Any ideas on how I can maintain the correct density?
> >
> > Thanks,
> >
> > Ilya
> >
> >
> > --
> > Ilya Chorny Ph.D.
>
>

-- 
Ilya Chorny Ph.D.

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