[gmx-users] genbox

David van der Spoel spoel at xray.bmc.uu.se
Sun Feb 1 10:51:09 CET 2009

Sunil Thapa wrote:
> Respectable Mark
> I am studying diffusion of oxygen in water. Can I specify the number of 
> water molecules for a particular size of box. For example, I need to 
> have 98 water molecules and 2 oxygen molecules in one solution. After 
> that I need to increase the number of oxygen molecules and decrease the 
> number of water molecules, viz, 10 oxygen molecules and 90 water molecules.
> What i have found so far is that genbox adds the number of water 
> molecules according to the size of the box. For cubical box of 1.5nm it 
> adds about 110 water molecules.
> Your help would be very helpful in this regard.

genbox -h

shows you that there is an option

genbox -maxsol

> Sunil Kumar Thapa
> Tribhuvan University, Nepal
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David van der Spoel, Ph.D., Professor of Biology
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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