[gmx-users] Place water away from existing atoms

[Steven Neumann]

On Thu, May 17, 2012 at 11:52 AM, Javier Cerezo <jcb1 at um.es> wrote:

>  genbox calculates overlaps based on vdW radii as included in vdwradii.dat
> in the topology folder. Increase the vdW radii of carbons to avoid water to
> closer that you want. Other possibilities are patiently removing undesired
> waters by hand after solvation or using a "ad-hoc" script.
>
> Javier
>

Thank you Javier. Can you please explain what is ad-hoc script and where I
can find it?

Steven



>
> El 17/05/12 12:25, Steven Neumann escribió:
>
> Dear Gmx users,
>
> My system consists of a tube which is representated by atoms which are not
> connected via bonds.
> genbox somehow place water molecules overlapping my tube atoms resulting
> in bad contacts.
>
> Is there anyway to add water e.g. 4A away from existing index file of my
> tube?
>
> Please, help.
>
> Steven
>
>
>
> --
> Javier CEREZO BASTIDA
> PhD Student
> Physical Chemistry
> Universidad de Murcia
> Murcia (Spain)
> Tel: (+34)868887434
>
> --
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