[gmx-users] genion problem: is replacing 84 water molecules instead of 200

[David van der Spoel]

Subhrangshu Supakar wrote:
> Hi All !!
> I have defined my own system which contains 200 water molecules, which I 
> can see in the .gro file. Then I created the .tpr file for 200 steps to 
> steep. In the confout file I can again see the 200 water molecules. But 
> When I am trying to replace the 200 water  molecules with 200 Na+ 
> GROMACS is complaining:

genion -h is your friend.

check the -rmin option.
> 
> Replacing solvent molecule 144 (atom 4632) with Na
> Replacing solvent molecule 193 (atom 4779) with Na
> Replacing solvent molecule 49 (atom 4347) with Na
> Replacing solvent molecule 84 (atom 4452) with Na
> 
> -------------------------------------------------------
> Program genion, VERSION 3.3.2
> Source code file: gmx_genion.c, line: 84
> 
> Fatal error:
> No more replaceable solvent!
> -------------------------------------------------------
>  It is replacing 84 water molecules only (I used genion for this)
> 
> Can any body help me?
> 
> Thanx in advance.
> 
> Subhrangshu Supakar
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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