Re: Controlling the area per lipid

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Thu Nov 01 2007 - 10:32:50 CDT

Does anyone have a script for calculating area/lipid. The way I currently do
it is get the minmax of the protein to estimate the area of the protein and
then subtract that area the box area caluclated using the XY cell basis
dimensions and then divide by the number of lipids per leaflet. I am
probably overestimating the protein area.

Thanks,

Ilya

On 11/1/07, Himanshu Khandelia <hkhandel_at_memphys.sdu.dk> wrote:
>
> Please be warned that if you use the CHARMM force field and the NPT
> ensemble, the membrane will NOT equilibrate to the correct area per lipid,
> the area will keep shrinking. The NPT ensemble is not best suited to
> simulate a membrane with the CHARMM force field.
>
> A good strategy might be to start with dimensions 10% larger than the
> known experimental area per lipid, and allow the area to shrink (in NPT)
> to the correct value area per lipid, and then fix the area of the bilayer
> and continue your simulation in the NPzAT ensemble.
>
> -Himanshu
>
> ----------------------------
> Himanshu Khandelia
> Research Assistant Professor (Postdoc),
> MEMPHYS, Center for BioMembrane Physics: www.memphys.sdu.dk
> University of Southern Denmark (SDU)
> Campusvej 55, Odense M 5230, Denmark
> Phone: +45 6550 3510, +45 2398 7972
> Fax: +45 6550 4048
> email: hkhandel_at_memphys.sdu.dk,
> hkhandelia_at_gmail.com
> WWW: www.memphys.sdu.dk/~hkhandel
> -----------------------------
>
>
>
> On Wed, 31 Oct 2007, Ilya Chorny wrote:
>
> > 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.
> >
>

-- 
Ilya Chorny Ph.D.

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