<div>Dear Gmx Users,</div>
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<div>I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow:</div>
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<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">1.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">First make your molecules whole if you want them whole </font></font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">2.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Cluster your molecules/particles if you want them clustered</font></font></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">3.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">4.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Remove jumps if you want to have them removed using the first frame</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">5.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Center your system using some criterion. Doing so shifts the system, so don't use </font></font><code><span style="FONT-SIZE: 10pt">trjconv -</span></code><span class="highlight"><span style="BACKGROUND: yellow"><font size="3" face="Times New Roman">pbc</font></span></span><code><span style="FONT-SIZE: 10pt"> nojump</span></code><font size="3" face="Times New Roman"> after this step.</font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">6.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Put everything in some box.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc</font></font></span></p>
<p style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 54pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto; mso-list: l0 level1 lfo1; tab-stops: list 54.0pt" class="MsoNormal"><font face="Times New Roman"><span style="mso-list: Ignore"><font size="3">7.</font><span style="FONT: 7pt 'Times New Roman'"> </span></span><font size="3">Fit if desired and don't use any <span class="highlight"><span style="BACKGROUND: yellow">PBC</span></span> related option afterwards.</font></font></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font face="Times New Roman">trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc</font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font color="#000000" face="Times New Roman"></font></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font color="#000000" face="Times New Roman">I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions?</font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font color="#000000" face="Times New Roman"></font></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt; mso-margin-top-alt: auto; mso-margin-bottom-alt: auto" class="MsoNormal"><span style="COLOR: red"><font size="3"><font color="#000000" face="Times New Roman">Steven</font></font></span></p>
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