From: Axel Kohlmeyer (
Date: Fri May 11 2007 - 07:46:23 CDT

On Fri, 11 May 2007, SMAHANE CHALABI wrote:


please don't cross-post to mailing lists when you
cannot expect the same people being subscribed on
the same mailing list (as it is the case in NAMD-l
and VMD-l).

SC> Dear all,
SC> How could I find a pdb, a psf and a topology file of air? I would like to
SC> create an air box, using VMD I have to enter these to do?

please find attached a pretty good approximation to air
for small problem sizes in classical MD.

for larger boxes you have to first specify what temperature/pressure
you are interested in (as you probably know, unlike liquids air changes
its volume a lot with temperature and pressure) and if you are
interested in a really, really large system, what ratio of nitrogen,
oxygen, co2, argon and relative humidity.


SC> Thanks very much!!
SC> Kind regards,
SC> Smahane.
SC> _________________________________________________________________
SC> Ten : Messenger en illimité sur votre mobile !

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.

  • chemical/x-pdb attachment: air.pdb