[gmx-users] genion to not continuous solvent

[Diego Enry]

Hello Yang,
I forgot to mention I did not want to use the random function.

I during the night I wrote a .f77+.sh to make reorder and reorganize
the coords and indexes. I'll make it more automatic user-friendly
(probably bash-only) and post it to contrib.

Now the question is if there's a way to make "g_dist" calculate and
write for me the residues within a certain distance of a group of
atoms. g_dist -h says it writes atom distances within a certain
distance of the "center of mass" of a reference group.

Diego Enry.


On 11/2/05, leafyoung81-group at yahoo.com <leafyoung81-group at yahoo.com> wrote:
> 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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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.