From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/5695.html.
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.

Best,
Peter

SMAHANE CHALABI wrote:
> 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.
>
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