<div>Thank you both!!!</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Mon, Oct 24, 2011 at 3:01 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 Steven,</p>
<p>Output can also be .pdb or .gro</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p>
<blockquote type="cite">
<div class="im">On Oct 24, 2011 3:59 PM, "Steven Neumann" <<a href="mailto:s.neumann08@gmail.com" target="_blank">s.neumann08@gmail.com</a>> wrote:<br><br>
<div>Sorry guys but I do not get this...</div>
<div> </div>
<div> </div>
<div>I used:</div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt"></span> </div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt">1. First make your molecules whole if you want them whole </span></div>
<div><span style="FONT-FAMILY: 'Times New Roman'; FONT-SIZE: 12pt"></span> </div>
<div>
<p style="MARGIN: 0cm 0cm 0pt" 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" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt" 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" 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" 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" 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" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" 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" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">4. How to use this frame in:</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p><span style="COLOR: #222222">
<p style="MARGIN: 0cm 0cm 0pt" 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" class="MsoNormal"><span style="COLOR: #222222"></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">Please, help!</span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222"></span> </p><font color="#888888">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="COLOR: #222222">Steven</span></p></font></span></span></font></font>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR: #222222"></span></font></font> </p><br><br></div></div>
<p><font color="#500050">On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>> wrote: > > Hi, > > You don't n...</font></p>
<div class="im"><br>--<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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></blockquote>
<p></p><br>--<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" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</p></blockquote></div><br>