[gmx-users] polyatomic ion additon by genion

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 16 12:17:38 CET 2008

kinshuk at chem.iitb.ac.in wrote:
> Hi all,
>   I have been trying to simulate peptide in water box with guanidium ion &
> thiocynate ion(SCN-).I tried to add these ion by genion command line by
> simply adding topology information of these ion in ions.itp of gromacs
> library directory but it is not working properly it only adds one atom
> by replacing water molecule it seems that genion is applicable only for
> monoatomic ion.
>   If i have to do simulation with these polyatomic ions with perticular
> salt concentration how do i will perform it.
with genbox. compute number yourself.
> Kinshuk
> IIT-Bombay
> India
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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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