[gmx-users] changing the code just a little bit (g_density)

[Marcelo A. Carignano]

I saw it now,

many thanks! Marcelo.

On Mon, 2005-11-21 at 14:55 +0100, Tsjerk Wassenaar wrote:
> 
> Hi Marcelo,
> 
> In Gromacs versions > 3.2.1 you can do this with trjconv -fit
> translation
> 
> Cheers,
> 
> Tsjerk
> 
> On 11/21/05, Marcelo A. Carignano <cari at purdue.edu> wrote:
>         it would be great if that's possible but I don't see how.
>         I see that I can shift the system by a vector using trjconv
>         -shift
>         by this shift is the same for all the frames.
>         My reference atom is moving too.
>         
>         Could you please explain more 
>         
>         Marcelo.
>         
>         On Mon, 2005-11-21 at 11:37 +0100, X.Periole wrote:
>         > On Fri, 18 Nov 2005 13:27:06 -0500
>         >   "Marcelo A. Carignano" <cari at purdue.edu> wrote: 
>         > > Dear Gromacs users,
>         > >
>         > >
>         > > I need to modify g_density so I can calculate the
>         > >density profile in
>         > > my system, but shifting the z coordenate so that one
>         > >particular atom
>         > > stays fix. Let's call "A" to this atom, then I need to
>         > >do (z-zA)
>         > > before calculating to which slice the current atom
>         > >belongs to.
>         > > 
>         >
>         > What about shifting your trajectory before using
>         > g_density?
>         > Make the atom fix using trjconv ...
>         >
>         > Best
>         > XAvier
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> 
> 
> -- 
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB) 
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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