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

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 30 15:51:26 CEST 2008

Quoting vips g <vipul_indian at rediffmail.com>:

> Hello,
>   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.

You can use genconf to make a box of gas molecules, and use genbox as you would
with water.  As for developing the parameters, you'll have to go to the
literature.  There is no singular way to do this.  Have a look here:


>   Does the force fields itp files contain parameters for oxygen and hydrogen
> gas molecule.

Not any of the ones that come standard with GROMACS.

>   How can i perform a simulation of protein surrounded by gases molecule. Is
> it possible with GROMACS.

I suppose anything is possible, given appropriate parameters.

>   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.

Generic descriptions of errors are not useful in helping us to help you.  What
were you doing when you got an error?  What was the *exact* command you issued
and the *exact* error message you received?


>  Kindly help me out.
>  Thanking you
> Vipul Gupta


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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