[gmx-users] using genion...

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 20 21:22:38 CET 2002

On Wed, 20 Mar 2002, Giorgos Karvounis wrote:

>Dear all,
>I am trying to insert a Na atom to the spc216 water model and run a
>simulation. I tried to use genion but im facing some problems with this
>command. I changed the .top by deleting one solvent molecule , inserting
>1 Na atom and #include "ions.itp".I am not quite sure though what do i
>have to change at the .gro or .pdb file. I would really appreciate if i
>could have some examples of the syntax of this command. I searched the
>archive and i found one more similar question about the use of genion
>but i couldnt trace the answer...
>...so once again any help is appreciated.
gro file is done by genion.
topology should be modifed as you specified.

It will be more automated later...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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