[gmx-users] solvent except water

[David van der Spoel]

rasoul nasiri wrote:
> Hi
> 
> I want to use a solvent with two types molecules (for example linear and 
> cyclic Glucose form).
> How can I fill box with them?

You can use genbox with  mixed solvents.
> 
> I highly appreciate for advice given me!
> 
> Best Regards
> Rasoul
> 
> On Sat, Jan 16, 2010 at 11:42 AM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> 
>     leila karami wrote:
> 
>         Dear David
>          in genbox command system solvated by water molecule by default.
>         but I want solvent except water.
>           leila karami
> 
>     OK, now I understand.
> 
>     You can give to genbox any solvent that you like, provided that each
>     molecule consists of a single residue (the residue number is used to
>     distinguish molecules).  In the gromacs distribution there are a
>     couple of other solvents present. Look in share/gromacs/top
>     directory of your installation (or roll your own).
> 
>     -- 
>     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 <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
>     -- 
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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