[gmx-users] how to run a gases diffusiion simulation

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 14 08:38:07 CET 2008

vips g wrote:
> hi to all
> i am currently using GROMACS to run a simulation of gases diffusion  
> that includes hydrogen and oxygen gas .
> I am stuck at the part in which I have to replace water with oxygen gas 
> using genbox command.
> I could no fond any .gro file for oxygen or hydrogen gas
> How I can include the gas in my simulation
> can any1 provide me any paper relating the use of gromacs for gases 
> diffusion simulation

you'll have to make it yourself. provided you have a good topology it is 
1. simulate single molecule
2. use genconf to multiply
3. simulate gas

> Thanking You
> Sincerely
> Vipul Gupta
> University of Allahabad
> India 
> Honda 
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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