<div>Sorry guys but I do not get this...</div>
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<div>I used:</div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"></span> </div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA">1. First make your molecules whole if you want them whole </span></div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt; mso-fareast-font-family: 'Times New Roman'; mso-ansi-language: EN-GB; mso-fareast-language: EN-GB; mso-bidi-language: AR-SA"></span> </div>
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<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">trjconv </span>-f md2.trr -s md2.tpr <span style="COLOR: #222222">-pbc whole -o md2whole.xtc (I have chosen my whole system for input and output)</span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">2. I do not need cluster anything</span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">3. </span></font></font><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"><font color="#000000">Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.</font></span></font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><font size="3"><font face="Times New Roman"><span style="COLOR: #222222">
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">trjconv </span><font color="#000000">-f md2whole.xtc -s md2.tpr </font><span style="COLOR: #222222">-dump 0 -o md2wholeDUMP.xtc ???</span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">I did not obtain any coordinate file as output can be only trajectory (trr or xtc file)</span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">4. How to use this frame in:</span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222"></span> </p><span style="COLOR: #222222">
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">trjconv </span><font color="#000000">-f md2wholeDUMP.xtc -s md2.tpr </font><span style="COLOR: #222222">-pbc nojump -o md2wholeDUMPnojump.xtc ?????</span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">Please, help!</span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: #222222">Steven</span></p></span></span></font></font>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><br><br></div>
<div class="gmail_quote">On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<p>Hi,</p>
<p>You don't need a .tpr file for removing jumps; a pdb/gro file will do.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p>
<blockquote type="cite">On Oct 24, 2011 2:51 PM, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>> wrote:<br><br>
<p><font color="#500050">Steven Neumann wrote: > > Dear Gmx Users, > I am trying to convert my trajectory using trjconv. ...</font></p>trjconv -dump 0
<p><font color="#500050">> > 3. Remove jumps if you want to have them removed using the first frame > > > trjconv -f traj...</font></p>
<div class="im">Recreate the .tpr file using the coordinate file produced in (2).<br><br>-Justin<br><br>-- <br>==============================<u></u>==========<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br><br>==============================<u></u>==========<br><font color="#888888">-- <br>
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