<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Really? This is really great! <div>Is there any need to specify the location of the vmd libraries? </div><div><br></div><div>If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this </div><div>somehow still possible? </div><div><br><div><div>On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">In case you use the GIT version of the analysis tools you don't need to convert the trajectories first.<div>I've added that the analysis tools can read all vmd supported file formats if GROMACS finds the vmd libraries.</div> <div><br></div><div>Roland<br><br><div class="gmail_quote">On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> <br> Well I guess you want to use gmx analysis tools so you'll have to<br> build the gmx topology of your system when necessary! Often<br> only a pdb file or a gro file is sufficient.<div><div></div><div class="h5"><br> <br> On Apr 16, 2010, at 5:24 PM, ram bio wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Thanks Xavier,<br> <br> Could you make it more eloborate...<br> <br> Ram<br> <br> On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>> wrote:<br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <br> VMD reads Desmond trajectories and writes GMX format ...<br> Rests the topology to deal with ...<br> <br> On Apr 16, 2010, at 4:15 PM, ram bio wrote:<br> <br> <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Dear All,<br> <br> I have run a dynamics of protein ligand complex in lipid bilayer dppc<br> using desmond software and would like to convert the trajectory files<br> files into gromacs format, is it possible?? if so, please let me know<br> your suggestions.<br> <br> Thanks,<br> <br> Ram<br> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. 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Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br> </div> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php</blockquote></div><br></div></body></html>