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

[David van der Spoel]

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 
easy.
1. simulate single molecule
2. use genconf to multiply
3. simulate gas

> Thanking You
> Sincerely
> Vipul Gupta
> IIDS
> University of Allahabad
> India 
> 
> 
> 
> Honda 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2066359_2058993/2066443/1?PARTNER=3&OAS_QUERY=null>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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