[gmx-users] simulation of gases diffusion pathways

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 29 21:54:46 CET 2008

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>
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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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