<br>
Hi Marcelo,<br>
<br>
In Gromacs versions > 3.2.1 you can do this with trjconv -fit translation<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 11/21/05, <b class="gmail_sendername">Marcelo A. Carignano</b> <<a href="mailto:cari@purdue.edu">cari@purdue.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
it would be great if that's possible but I don't see how.<br>I see that I can shift the system by a vector using trjconv -shift<br>by this shift is the same for all the frames.<br>My reference atom is moving too.<br><br>Could you please explain more
<br><br>Marcelo.<br><br>On Mon, 2005-11-21 at 11:37 +0100, X.Periole wrote:<br>> On Fri, 18 Nov 2005 13:27:06 -0500<br>> "Marcelo A. Carignano" <<a href="mailto:cari@purdue.edu">cari@purdue.edu</a>> wrote:
<br>> > Dear Gromacs users,<br>> ><br>> ><br>> > I need to modify g_density so I can calculate the<br>> >density profile in<br>> > my system, but shifting the z coordenate so that one<br>
> >particular atom<br>> > stays fix. Let's call "A" to this atom, then I need to<br>> >do (z-zA)<br>> > before calculating to which slice the current atom<br>> >belongs to.<br>> >
<br>><br>> What about shifting your trajectory before using<br>> g_density?<br>> Make the atom fix using trjconv ...<br>><br>> Best<br>> XAvier<br>> _______________________________________________<br>
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<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>