From: Peter Freddolino (
Date: Thu May 10 2007 - 10:25:46 CDT

Hi Smahane,
you need to decide whether you want an "air box" or just vacuum, for the
tails, because at MD length scales there really isn't a whole lot there
for air. If you truly want an air box, you might want to follow the
advice given at
You'll need to generate the initial coordinates for the molecules in the
"air" portion; one could do this, for example, by using solvate with a
nonstandard solvent -- an air box (see the solvate documentation for
details). You would need to generate the air box yourself, though.


> Hi all,
> I would to do a phospholipid monolayer with the absorbent head in a
> water box and hydrophobic tails in a air box, is it possible? if yes,
> how could I generate this air box by VMD? Or is this one automatically
> generated, by default?
> Kind Regards,
> Smahane.
> _________________________________________________________________
> Windows Live Spaces : créez votre blog à votre image !