[gmx-users] Ion positioning 2

[David]

On Mon, 2002-07-08 at 15:26, Lieven Buts wrote:
>   I tried my genion run again without
> using the "-bt dodecahedron" option for
> editconf. Now the ions are all around the 
> protein (<http://ultr.vub.ac.be/~lieven/ions2.png>),
> so the problem would seem to have something to do
> with the box shape. 
You definitely want to use the -random option for genion along with the
cutoff (as large as can be). The potential doesnä't work well.


> 
> -- 
> Lieven Buts
> Vrije Universiteit Brussel
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-- 
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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