<div>Thank you all! That helped a lot!</div>
<div> </div>
<div>Steven<br><br></div>
<div class="gmail_quote">On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz <span dir="ltr"><<a href="mailto:durmaz@zib.de">durmaz@zib.de</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><u></u>
<div bgcolor="#ffffff" text="#000000">i always did it (successfully) with one single command:<br><br>trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n ../../index.ndx <br><br><br>regards<br>vedat<br><br>
<br>Am 29.02.2012 18:01, schrieb Steven Neumann:
<div>
<div class="h5">
<blockquote type="cite">
<div>Dear Gmx Users,</div>
<div> </div>
<div>I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The problem I face is PBC which I cannot get rid of. I used:</div>
<div> </div>
<div>
<p style="MARGIN:0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span style="COLOR:gray" lang="EN-GB"><span><font size="3">1.</font><span style="FONT:7pt 'Times New Roman'"> </span></span></span><span style="COLOR:gray" lang="EN-GB"><font size="3">First make your molecules whole if you want them whole (system).</font></span></font></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><font size="3"><font face="Times New Roman"><span style="COLOR:red" lang="EN-GB">trjconv -f </span><span style="COLOR:red" lang="PL">md298SKIP4.xtc </span><span style="COLOR:red" lang="EN-GB">-s md298.tpr -pbc whole -o md298whole.xtc </span></font></font></p>
<p style="MARGIN:0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span style="COLOR:gray" lang="EN-GB"><span><font size="3">2.</font><span style="FONT:7pt 'Times New Roman'"> </span></span></span><span style="COLOR:gray" lang="EN-GB"><font size="3">Cluster your molecules/particles if you want them clustered</font></span></font></p>
<p style="MARGIN:0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span style="COLOR:gray" lang="EN-GB"><span></span></span></font> </p>
<p style="MARGIN:0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span style="COLOR:gray" lang="EN-GB"><span><font size="3">3.</font><span style="FONT:7pt 'Times New Roman'"> </span></span></span><span style="COLOR:gray" lang="EN-GB"><font size="3">Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.</font></span></font></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"><font size="3"><font face="Times New Roman">trjconv -f md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt 54pt" class="MsoNormal"><font face="Times New Roman"><span style="COLOR:rgb(153,153,153)" lang="EN-GB"><span><font size="3">4.</font><span style="FONT:7pt 'Times New Roman'"> </span></span></span><span style="COLOR:rgb(153,153,153)" lang="EN-GB"><font size="3">Remove jumps if you want to have them removed using the first frame (system)</font></span></font></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"><font size="3"><font face="Times New Roman">trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"><font size="3"><font color="#000000" face="Times New Roman">So the trajecory of my ligands is smooth but they do do bind to the different periodic images. As i know it is impossible to obtain the proper trajectory of all of them I just want to obtain the realistic final positions of my system to extract pdb file for further umbrella sampling. Any suggestions?</font></font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"></span> </p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"><font color="#000000" size="3" face="Times New Roman">Steven</font></span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"></span> </p></div></blockquote></div></div></div><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>
</blockquote></div><br>