Thank you all for your replies. Stephan -- can you explain a little more about your 5 line bash script idea? The only part I am not sure about is pulling out the water molecules within a certain distance. Are you suggesting to write a script that calculates atom distance and saves only those within a defined distance?
Thanks, Blake -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of lloyd riggs Sent: Tuesday, June 05, 2012 10:52 AM To: [email protected]; Discussion list for GROMACS users Subject: Re: [gmx-users] Trajectories 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" <[email protected]> > An: Discussion list for GROMACS users <[email protected]> > 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 [email protected] > 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 [email protected]. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
