Hi,<br><br><div><span class="gmail_quote"></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I try to remove the periodicity</blockquote>
<div><br>You don't remove periodicity. -pbc nojump removes jumps due to (over) the PBC, not the PBC itself.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
to get a new .xtc file and one .gro<br>file. The commands are shown below:<br>"trjconv -f original.xtc -s original.tpr -n index -o frame_0.gro -dump 0<br>-pbc nojump"</blockquote><div><br>Since your frame_0 will hold the same coordinates as your .tpr file, -pbc nojump serves no purpose here.
<br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> "trjconv -f original.xtc -s original.tpr -n index -o new.xtc -pbc<br>nojump"
<br>When I use g_rms to calculate the rmsd by new .xtc and .gro file, there<br>is a warning and other things goes well. Command i used is "g_rms -f<br>new.xtc -s frame_0.gro -o rmsd.xvg" and the warning is "can not make
<br>broken molecules whole without a run input file,don't worry, mdrun<br>doesn't write broken molecules". I think i have removed the boundary,<br>and why it says there is an broken protein?</blockquote><div>
<br>It doesn't say there's a broken molecule. It says it couldn't fix one if it were present, because you don't provide topology information. But it also says that an .xtc file generated by mdrun (and not otherwise processed) doesn't contain broken molecules.
<br></div><br>Cheers,<br><br></div>Tsjerk<br>-- <br>Tsjerk A. Wassenaar, 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