From: Axel Kohlmeyer (
Date: Thu May 10 2007 - 09:22:45 CDT

On Thu, 10 May 2007, SMAHANE CHALABI wrote:

SC> Hi all,


hmmmm.... the concept of an 'air' box is a bit odd for
the size of systems you are typically looking at with
classical MD. have you tried to calculate how many 'air'
molecules your air box would contain? generally, one just
uses vacuum.

SC> I would to do a phospholipid monolayer with the absorbent head in a water
SC> box and hydrophobic tails in a air box, is it possible? if yes, how could I
SC> generate this air box by VMD? Or is this one automatically generated, by
SC> default?

in case of half water, half vacuum box, you can try setting
up a bilayer and then remove half of the system. as with all
layers, you have to be very careful when equilibrating this,
so you don't destroy its structure at the boundaries. in case
of a monolayer even more so.

the available tutorial material on the VMD and NAMD homepages
should present the techniques required to do this.


SC> Kind Regards,
SC> Smahane.
SC> _________________________________________________________________
SC> Windows Live Spaces : créez votre blog à votre image !

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.