From: Axel Kohlmeyer (
Date: Sat Jun 11 2011 - 10:21:45 CDT

On Sat, Jun 11, 2011 at 10:12 AM, sarah k <> wrote:
> Dear VMD users,
> Is it possible to simulate a protein in a nitrogen gas box by NAMD? If yes,
> How? If no, is there any other solution, software or idea? Thanks.

how high of a pressure of nitrogen do you expect to model?

how is the nitrogen supposed to impact the protein, if at all?

technically, it is of course possible, but before you do this,
please do a back of the envelope calculation:
- assume the nitrogen is an ideal gas
- the desired pressure and volume of your gas box
- calculate how many nitrogen atoms would be in that box


> Best regards,
> Fatemeh Keshavarz

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.