Hi Jaowei Tang,<br><br>Better use a .pdb or .gro file. Maybe the starting structure (obtained after running pdb2gmx)?<br>By the way, if you removed the jumps over the boundary (you don't really want to remove periodicity :p) you must already have a proper structure. Or you can then extract the first frame from the trajectory and use that as the starting point.
<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 10/4/07, <b class="gmail_sendername">tangxuan</b> <<a href="mailto:tangxuan82@gmail.com">tangxuan82@gmail.com</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;">
Dear all,<br>I am try to use g_rms to a protein, but its start structure in the<br>simulation is not in one box. I removed the periodicity for the xtc file<br>by trjconv, but do not know how to remove the periodicity in the tpr
<br>file. Could you give me some suggestions?<br><br>Thank you.<br><br>Jiaowei Tang<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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