<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>And even if not all orientations are exactly equal in this respect, bare in mind that the solute might rotate during the simulation, taking it out of any optimum.</div><div><br></div><div>Erik</div><div><br><div><div>26 apr 2012 kl. 14.36 skrev Tsjerk Wassenaar:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hey Thomas,<br><br>The rhombic dodecahedron corresponds to the packing of a sphere.<br>Consequently, the difference in the distance between periodic images<br>over the shortest diameter and the longest diameter is pretty small.<br>That means that there isn't really an optimal orientation in a rhombic<br>dodecahedron; all orientations are pretty much equal. And that's how<br>it should be :)<br><br>Cheers,<br><br>Tsjerk<br><br>On Thu, Apr 26, 2012 at 1:18 PM, Thomas Evangelidis <<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>> wrote:<br><blockquote type="cite">Dear GROMACS users,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have noticed that for constant box dimensions the minimum distance from<br></blockquote><blockquote type="cite">the periodic images of a protein depends on the initial orientation of the<br></blockquote><blockquote type="cite">protein, whereas the orientation of the dodecahedron relative to the x,y,z<br></blockquote><blockquote type="cite">axes remains fixed. These are the command lines I use:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">pdb2gmx_d4.5.5 -f protein.pdb -o protein.gro -p protein.top -ff<br></blockquote><blockquote type="cite">amber99sb-ildn -water tip3p -ignh<br></blockquote><blockquote type="cite"># set the new dodecahedron box dimensions<br></blockquote><blockquote type="cite">editconf_d4.5.5 -f protein.gro -bt dodecahedron -box 13 -o protein_box.gro<br></blockquote><blockquote type="cite"># solvate with TIP3P<br></blockquote><blockquote type="cite">genbox_d4.5.5 -cp protein_box.gro -cs spc216.gro -o protein_box_solv.gro -p<br></blockquote><blockquote type="cite">protein.top<br></blockquote><blockquote type="cite"># add ions<br></blockquote><blockquote type="cite">grompp_d4.5.5 -f em_real.mdp -c protein_box_solv.gro -p protein.top -o<br></blockquote><blockquote type="cite">protein_ions.tpr<br></blockquote><blockquote type="cite">echo 13 | genion_d4.5.5 -s protein_ions.tpr -o protein_EM.gro -p protein.top<br></blockquote><blockquote type="cite">-pname NA -nname CL -np 3<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">grompp_d4.5.5 -f em_real.mdp -c protein_EM.gro -p protein.top -o<br></blockquote><blockquote type="cite">protein_EM.tpr<br></blockquote><blockquote type="cite">mpirun -np 2 mdrun_d4.5.5 -v -deffnm protein_EM<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"># to see a dodecahedron<br></blockquote><blockquote type="cite">echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f protein_EM.trr -s<br></blockquote><blockquote type="cite">protein_EM.tpr -o em_dodecahedron.xtc<br></blockquote><blockquote type="cite"># measure the minimum distance from the periodic images<br></blockquote><blockquote type="cite">echo 1 | g_mindist_d4.5.5 -f em_dodecahedron.xtc -s protein_EM.gro -pi<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Is there any way to optimize the orientation of protein inside the<br></blockquote><blockquote type="cite">dodecahedron in order to get the maximum possible mindist?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks in advance,<br></blockquote><blockquote type="cite">Thomas<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">======================================================================<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thomas Evangelidis<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">PhD student<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Biomedical Research Foundation, Academy of Athens<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">4 Soranou Ephessiou , 115 27 Athens, Greece<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">email: <a href="mailto:tevang@bioacademy.gr">tevang@bioacademy.gr</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"> <a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">website: <a href="https://sites.google.com/site/thomasevangelidishomepage/">https://sites.google.com/site/thomasevangelidishomepage/</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--<br></blockquote><blockquote type="cite">gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br></blockquote><blockquote type="cite"><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br></blockquote><blockquote type="cite">Please search the archive at<br></blockquote><blockquote type="cite"><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br></blockquote><blockquote type="cite">Please don't post (un)subscribe requests to the list. Use the<br></blockquote><blockquote type="cite">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote><blockquote type="cite">Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote><br><br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<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">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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