[gmx-users] bilayer area questions WITH DATA
David
spoel at xray.bmc.uu.se
Wed Sep 14 22:10:37 CEST 2005
On Wed, 2005-09-14 at 12:06 -0700, Rama Gullapalli wrote:
> 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?
>
Of course there are 64. It is periodic boundary conditions that takes
care of this. A molecule that sticks out on one side in fact has e.g.
its tail on the other side of the box.
> 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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> > --
> > 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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--
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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