[gmx-users] bilayer area questions WITH DATA

[Rama Gullapalli]

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?

I really appreciate any replies in this regard.

Sincerely
Rama

--- "Dallas B. Warren"
<Dallas.Warren at vcp.monash.edu.au> wrote:

> > 1) Is it normal for a lipidbilayer to EXPAND after
> 
> > equilibriation? (From 5.5 by 5.4 to 7.4 to 7.8,
> NPT
> > compling)
> 
> Depends on large number of factors, main one being
> whether the starting
> bilayer is actually at the correct density/head
> group area or not.  If
> too small, then of course it will expand until it
> reaches around the
> equilibrium area.
> 
> > 2) How does one calculate the area per lipid ? (is
> it
> > as simple as multiply length of box x by box y and
> > divide by number of lipids?)
> 
> That is the standard way to do it, and from what I
> can tell, pretty much
> the only way.
> 
> > 3) How do i deal with the fact that my box size is
> > same as original, but system has expanded, if i
> want
> > to calculate the area per lipid?
> 
> How can the box size be the same as the originaly,
> when infact you have
> stated that the dimensions of the box in the x-y
> plane has actually
> expanded?
> 
> Catch ya,
> 
> Dr. Dallas Warren
> Lecturer
> Department of Pharmaceutical Biology and
> Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9073
> ---------------------------------
> When the only tool you own is a hammer, every
> problem begins to resemble
> a nail.
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