# [gmx-users] bilayer area questions WITH DATA

David spoel at xray.bmc.uu.se
Wed Sep 14 18:38:58 CEST 2005

```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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