[gmx-users] bilayer area questions WITH DATA

[Rama Gullapalli]

Dear David
thanks again. Sorry to belabour the point, i promise
to ask no more questions on this issue..:)

But, if the lipid molecules are sticking out of the
box, that means that there are not 64 molecules within
the size of the box right (<64)? And if that is true,
how can we assign the area per lipid to be the area of
the box divided by 64?

I hope im not being too dense...
Sincerely
Regards
Rama

--- David <spoel at xray.bmc.uu.se> wrote:

> On Wed, 2005-09-14 at 11:23 -0700, Rama Gullapalli
> wrote:
> > Dear David
> > Thanks for the reply. Maybe im not getting this
> > straight, But this was the inital box volume too,
> > since i have scaled the value of the vectors of
> the
> > box to be this at the beginning of the simulation.
> > 
> > Putting it another way, does the size of the
> system
> > have NOTHING to do with the box size and as a
> result,
> > the area per lipid ?....
> size of the system is quite meaningless as it
> includes molecules
> sticking out of the box which can be a lot with
> lipids.
> > 
> > I did plot the value of the length of the box x vs
> > time and length of box y vs time and as i expected
> it
> > is hovering around the values of the initial
> values of
> > the box. 
> > 
> > But the system is 7.8 by 8.1 so isnt the area per
> > lipid equal to 7.8 *8.1/ 64 for a 128 lipid
> system?
> > 
> > or is it still 5.6 * 5.8 / 64?
> Yes.
> 
> > 
> > Im quite throughly confused.
> > Thanks for your time and patience :)
> > Regards
> > Rama
> > 
> > 
> > --- David <spoel at xray.bmc.uu.se> wrote:
> > 
> > > On Wed, 2005-09-14 at 09:12 -0700, Rama
> Gullapalli
> > > wrote:
> > > > Dear Dr Warren
> > > > Thank you for your replies. Here is the data
> which
> > > i
> > > > got for the whole equilibriation process which
> is
> > > > causing me the confusion.
> > > > 
> > > > 1) After 100 picoseconds of equilibriation
> > > > new system size :  6.346  6.414  8.734
> > > > new center      :  2.949  2.909  4.294 (nm)
> > > > new box vectors :  5.847  5.762  8.600 (nm)
> > > > new box angles  :  90.00  90.00  90.00
> (degrees)
> > > > new box volume  : 289.74               (nm^3)
> > > > 
> > > > 2) After 2 nanoseconds of equilibriation
> > > > 
> > > > new system size :  8.032  7.517  8.685
> > > > new center      :  2.866  2.906  4.259 (nm)
> > > > new box vectors :  5.736  5.915  8.539 (nm)
> > > > new box angles  :  90.00  90.00  90.00
> (degrees)
> > > > new box volume  : 289.69               (nm^3)
> > > > 
> > > > 3) After 10 nanoseconds of equilbriation
> > > > 
> > > > new system size :  7.368  8.177  8.785
> > > > new center      :  2.881  2.936  4.316 (nm)
> > > > new box vectors :  5.692  5.876  8.640 (nm)
> > > > new box angles  :  90.00  90.00  90.00
> (degrees)
> > > > new box volume  : 288.95               (nm^3)
> > > > 
> > > > As you can see, the box size has remained
> > > constant,
> > > > but the system size has increased
> progressively
> > > and
> > > > the seems to begin to decrease too.
> > > > 
> > > > So my question is do i need to keep
> equilibriating
> > > the
> > > > system till it reaches the original size or is
> > > there
> > > > something i can do right at the outset(like
> > > specify
> > > > the density in editconf) so that the system
> does
> > > not
> > > > expand.
> > > > 
> > > > Also, why do the box vector sizes do not
> increase?
> > > The volume is constant and the box vectors have
> > > stabilized. Plot the box
> > > vectors as a function of time to check
> equilibration
> > > (using g_energy)
> > > 
> > > 
> > > -- 
> > > David.
> > >
> >
>
________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof.,
> Molecular
> > > Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala
> > > University.
> > > Husargatan 3, Box 596,          75124 Uppsala,
> > > Sweden
> > > phone:  46 18 471 4205          fax: 46 18 511
> 755
> > > spoel at xray.bmc.uu.se    spoel at gromacs.org  
> > > http://xray.bmc.uu.se/~spoel
> > >
> >
>
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> > 
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> -- 
> David.
>
________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular
> Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala
> University.
> Husargatan 3, Box 596,          75124 Uppsala,
> Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  
> http://xray.bmc.uu.se/~spoel
>
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