[gmx-users] to create a simulation box containing only oxygen gas

vips g vipul_indian at rediffmail.com
Sun Mar 30 15:22:44 CEST 2008

  I want to build a cubic simulation box of 0.9 nm containing oxygen gas molecule as a solvent.
  How can I make the box and develop its parameters.  
  Does the force fields itp files contain parameters for oxygen and hydrogen gas molecule.
  How can i perform a simulation of protein surrounded by gases molecule. Is it possible with GROMACS. 
  I have read the paper "PATHWAYS OF H2 TOWARDS THE ACTIVE SITE OF [NiFe]-HYDROGENASE" by Vitor H. Teixeira, António M. Baptista, Cláudio M. Soares published in Biophysics in 2006 in which they have used gromacs for performing simulation of hydrgen gas. They replaced randomly water molecules with hydrogen gas molcules. I have performed the same procedure but I am stuck at the step where it giving error of not recognising the gas molecule.
 Kindly help me out.
 Thanking you 
Vipul Gupta
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