[gmx-users] genion to not continuous solvent

[leafyoung81-group at yahoo.com]

Try -random?

Yang Ye

--- Diego Enry <diego.enry at gmail.com> wrote:

> Dear list,
> I am having an issue with genion and hope you guys
> could help me.
> 
>    Genion is working great , but one of the water
> molecules it
> replaces was supposed to be a part of a
> water-mediated H-bond like the
> one we see at HIV protease, so I really want that
> molecule to remain
> over there.
> 
>    The problem is that genion does not allow me to
> simply hide this
> water molecule by creating a new .ndx entry (14
> SOL_but_not_my_water) 
> without having to reorder and renumber the SOL atoms
> in the .gro file,
> placing this water in the end.
> 
>    For sure one molecule is no problem and I already
> did it, but if I
> had a bunch of systems in this situation ? Is there
> any trick to make
> this automatic ?
> 
> Diego Enry
> 
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
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