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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:
<blockquote
cite="mid:CAKZJqQFcaffH+i06CkekTaW7SCOTKj_Od86dSJewoPFQOp3hnw@mail.gmail.com"
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 style=""><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 style=""><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 style=""></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 style=""><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 style=""><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"
face="Times New Roman" size="3">Steven</font></span></p>
<p style="margin: 0cm 0cm 0pt;" class="MsoNormal"><span
style="color: red;" lang="EN-GB"></span> </p>
</div>
</blockquote>
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