Re: Controlling the area per lipid

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Nov 01 2007 - 00:56:27 CDT

Minmax measurements of lipids will not be reliable. Lipids that
stick out of the simulation cell will still be measured because they
don't get wrapped until most of the molecule crosses the periodic
boundary. The water will be more accurate, but the numbers in the
xst file will be the exact cell size over the simulation. If you are
using constant area, the x-y numbers should never change.

You should consider during initial equilibration though that the
membrane may shrink (and may need to), especially if you put a
protein in the middle and removed all lipids near it. After that,
you could run constant area though.

On Oct 31, 2007, at 8:23 PM, Ilya Chorny wrote:

> Hi I am having some trouble controlling the area per lipid molecule
> in my simulation. I set my cell basis vector in the XY plane to the
> correct area to maintain the proper density but the minmax
> measurements of my lipid give me values that are larger than the
> cell basis vectors. I also you constant area pressure coupling.
> Why is that? Any ideas on how I can maintain the correct density?
>
> Thanks,
>
> Ilya
>
>
> --
> Ilya Chorny Ph.D.

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