Dear Rankinib, You can do it with a 5 line bash script as well, cat everything times x,y,z and just cut and past them into a spread sheet, and save it with tabs or spaces.
Stephan Watkins -------- Original-Nachricht -------- > Datum: Tue, 05 Jun 2012 09:05:09 -0400 > Von: "Justin A. Lemkul" <jalem...@vt.edu> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Trajectories > > > On 6/5/12 9:02 AM, rankinb wrote: > > I am interested in pulling out the trajectories (x,y,z coordinates) of > water > > molecules within a certain distance of my solute molecule. I have tried > > using g_select, but that will only give me the atom numbers and not the > > trajectories. I can create an index file using this command but > > unfortunately each time frame is set as a different group. > > > > Is there a way to get the trajectories at all frames of only the water > > molecules within a specified distance of a solute molecule? > > > > At present, there is no elegant way to construct such a trajectory, since, > in > principle, each frame can have a different number of atoms based on which > water > molecules satisfy the given criteria. Each index group that g_select > provides > corresponds to an individual frame in the original trajectory, which you > can use > to pull out individual coordinate files. Perhaps a multi-frame .pdb or > .gro > file would work, but I believe that .xtc and .trr files have to have the > same > number of atoms in each frame to be interpreted correctly. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
