[gmx-users] simulation of gases diffusion pathways

[David van der Spoel]

vips g wrote:
> Hello users,
>   I am trying to simulate Hydrogen and Oxygen gas diffusion pathways in 
> a protein.
> First I have simulated the protein in a water bath for 50 ps .
> Now I want to simate it in a box containing either only gas molecule or 
> both gas+water molecule.
> I have used genbox to replace some water molecule randomly with hydrogen 
> gas molecule.
> The problem is that when I am prepairing the top file fo this system it 
> is not identifying the hydrogen gas molecule.
> Please tell me the way by which I can do this simulation.
> Kindly also tellme about some papers related to this work.
> Sincerely

you will have to do literature search yourself.
most likely hydrogen is going to be difficult.



> Vipul Gupta
> 
> 
> 
> ICL 
> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/2076213_2068813/2076295/1?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