<html><head></head><body bgcolor="#FFFFFF"><div><span class="Apple-style-span" style="-webkit-tap-highlight-color: rgba(26, 26, 26, 0.296875); -webkit-composition-fill-color: rgba(175, 192, 227, 0.230469); -webkit-composition-frame-color: rgba(77, 128, 180, 0.230469); ">On 1 Mar, 2012, at 1:01, Steven Neumann <<a href="mailto:s.neumann08@gmail.com">s.neumann08@gmail.com</a>> wrote:</span><br></div><div><br></div><div></div><blockquote type="cite"><div><div>Dear Gmx Users,</div>
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<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>
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<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=""><font size="3"></font></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:#999999" lang="EN-GB"><span style=""><font size="3">4.</font><span style="FONT:7pt 'Times New Roman'"> </span></span></span><span style="COLOR:#999999" 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"><font size="3"><font face="Times New Roman"></font></font></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></div></div></blockquote><div><br></div>You may wanna try <div><br></div><div>Trjconv -f <span lang="PL">md298SKIP4.xtc </span><span lang="EN-GB">-s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000</span></div><div><br></div><div>Please change dt if necessary. <br><div><br></div><div><br><blockquote type="cite"><div><div>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style="COLOR:red" lang="EN-GB"><font color="#000000" size="3" face="Times New Roman"></font></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"><font color="#000000" size="3" face="Times New Roman"></font></span> </p></div>
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