Hi Tang,<br><br>It doesn't hurt to check (i.e. you should check ;)) whether the .tpr file contains the protein "in one piece", if you want to use it as a reference structure for rmsd calculations. You can extract the coordinates from the .tpr file using editconf and then have a look. Actually, you should've done this prior to removing jumps from the trajectory, since you must be sure to remove the jumps in the right way (check the archives for more discussion on these issues).
<br><br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Dec 12, 2007 1:42 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">tangxuan wrote:<br>> hi all,<br>> I want to calculate the rmsd of my protein. If I remove the jump in the<br>> xtc file or trr file, what should I do with tpr file?<br><br></div>Nothing. Depending on your inputs to g_rms, it might provide your
<br>reference structure.<br><font color="#888888"><br>Mark<br></font><div><div></div><div class="Wj3C7c">_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623