[gmx-users] GENION: Ions inside the protein

Viswanadham Sridhara muta.mestri at gmail.com
Tue Oct 10 18:28:19 CEST 2006

you might have deleted just one atom of water molecule.
Ex: If you are using SPC water , you have to delete all 3 atoms in index

Best way is to make changes in .gro file..
Renumber the resulting .gro file using genconf, make a new index file and
start running.

On 10/10/06, Una Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:
> Dear users,
> In some of my simulations after neutralizing the systems with genion 2
> of the ions were inside the active site cleft of the protein.
> In the discussion on the list it was commented to either delete the
> solvent within the protein which I did I deleted the water molecule
> (11798) and gave genion that index file as input but than this error came:
> Fatal error: The solvent group is not continuous: index[8198]=11797,
> index[8199]=11799
> I don't want to use the -random command in genion if possible because in
> none of the other simulations I have used it.
> Is there any other way to delete the solvent within the protein did I
> misunderstand that so those water molecules will not be replaced?
> Best regards, Una Bjarnadottir
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Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.
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