[gmx-users] Lipid area calculation

[Pedro Alexandre Lapido Loureiro]

Surlignage Yuhua Song <yhsong at ccb.wustl.edu>:

> Thanks David. I use the way that you describe to calculated the lipid area,
> I gets the reasonable lipid area. From the literature, its seems that
> another parameter need to validate is volume/lipid. Now, I have box_x,
> box_y, box_z, I get the total volume. if I want to calcuate the
> volume/lipid, I assume that I shoud be: (total volume-water volume)/#total
> lipids. Am I right? If I am right, how could get the water volume? from
> literature, it said that SPC water 1.03g cm^-3 at 323 K. Now, I only know
> that number of water in my system, how can I know one water volume? If my
> way to calculate the volume/lipd is not right. Could you please give me
> some
> suggestion?
> 
> Thanks,
> 
> Yuhua
> 
> 
> 
> 
>
Yes, you are right about lipid volume. 
Here is a suggestion to calculate water specific volume:
-perform a constant pressure simulation of a pure water box at the same 
temperature you are using for your lipid system.
-after equilibration, divide the box volume/number of water molecules.
-you will have SPC water specific volume.

Cheers,

Pedro.

--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil