[gmx-users] bilayer area questions WITH DATA

[Rama Gullapalli]

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 ?....

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?

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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