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

[Tsjerk Wassenaar]

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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