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</o:shapelayout></xml><![endif]--></head><body lang=DE link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Or you could use trjconv in a little script to convert the snapshots you like to .pbd. Use the –b and –e flags to choose the respective time points.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Also see <a href="http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts">http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts</a> for the use trjconv non-interactively.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Good luck.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>Von:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>Im Auftrag von </b>aiswarya pawar<br><b>Gesendet:</b> Mittwoch, 18. Januar 2012 07:53<br><b>An:</b> Discussion list for GROMACS users<br><b>Betreff:</b> Re: [gmx-users] Regarding trajectory file<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>You can write this on VMD forum. Anyways you can try by doing this in the Tcl console-<o:p></o:p></p><pre>set sel [atomselect top "solvent"]<br>$sel get {x y z}<o:p></o:p></pre><p class=MsoNormal style='margin-bottom:12.0pt'>This would give you the coordinates of the solvent, for your purpose you got to iterate so as to get for each time step.<br><br><br>Aiswarya<br>SERC Dept, IISc<br>Bangalore<br><br><br><o:p></o:p></p><div><p class=MsoNormal>On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<o:p></o:p></p><div><p class=MsoNormal>On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:<o:p></o:p></p><p class=MsoNormal><br>Dear All,<br> I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using VMD or any other viewer.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>You're unlikely to get help for non-GROMACS software on this mailing list. Check out manual section 7.4 for clues on what GROMACS tools might help, and then section 8 and appendix D for more details.<span style='color:#888888'><br><br><span class=hoenzb>Mark</span><br><span class=hoenzb>-- </span><br><span class=hoenzb>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a></span><br><span class=hoenzb><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span class=hoenzb>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br><span class=hoenzb>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.</span><br><span class=hoenzb>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></span></span><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></body></html>