Hi Morteza,<br> I had this problem when I was running a trimeric protein attached to an oligosaccharide.<br><br><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><b><span><font face="Times New Roman">I have used the following command:</font></span></b></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><b><span><font face="Times New Roman"> </font></span></b></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><b><span><font face="Times New Roman">trjconv<span> </span>-s .tpr -f .xtc -o<span> </span>-boxcenter tric -pbc mol</font></span></b></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><b><span><font face="Times New Roman"> </font></span></b></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><b><span><font face="Times New Roman">but it is not working.</font></span></b></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;">
<span><font face="Times New Roman">Do the following. It worked for me.</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">In the first round, run</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">trjconv -f *.xtc -s *.tpr -center -boxcenter tric -pbc mol -o 1.xtc</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">and choose backbone (which is usually 4 from the index) for centring.</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">In the second round,</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;">
<span><font face="Times New Roman">use 1.xtc obtained from the first step and run the command as follows<br></font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;">
<span><font face="Times New Roman">trjconv -f 1.xtc -s *.tpr -center -boxcenter tric -pbc a -o 2.xtc</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">and this time also choose the backbone for centring.<br>
</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">This should bring back the dimeric protein system in the box. Sometimes the water molecules around the edge are broken. Hope this is not a big worry.<br>
</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">By the way is your box cubic or truncated octahedron?</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">My case was a cubic box.</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;">
<span><font face="Times New Roman">Hope this helps.</font></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><br><span></span></p><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Regards</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Sai<br></font></span></p><br><br><div class="gmail_quote">On Tue, Jun 8, 2010 at 2:23 AM, shahab shariati <span dir="ltr"><<a href="mailto:shahab.shariati@gmail.com">shahab.shariati@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Morteza Khabiri wrote:</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Dear users</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">I have a dimer protein in the water box. It was run for 30ns.</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">during the simulation dimer split to two monomer. This things happen bc of</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">PBC. ( I checked it by vmd pbc option )</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">to have a two monomer together during trajectories (for visualization)</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">I have used the following command:</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">trjconv<span> </span>-s .tpr -f .xtc -o<span> </span>-boxcenter tric -pbc mol</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">but it is not working.</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Is there any other method or command which I could implement pbc in</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">trajectory.</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Thanks in advance</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Morteza</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Shahab Shariati wrote:</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">You can use other flags of trjconv command as follows:</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman">Trjconv –f *.xtc –s **.tpr –o ***.xtc –pbc nojump –ur compact -center</font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<p class="MsoNormal" style="margin: 0cm 0cm 0pt;"><span><font face="Times New Roman"> </font></span></p>
<br>--<br>
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