<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>you need to do:<div><br></div><div>1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction<br><div><div>2- trjconv -center; using the bilayer to center and the system as output; this will </div><div>translate your bilayer on the z axis and normally not modify it on the xy plan. </div><div>3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this </div><div>step cn be coupled to the previous quite safely.</div><div><br></div><div>On Nov 5, 2009, at 3:23 PM, maria goranovic wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system<br><br> <div class="gmail_quote">On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic <span dir="ltr"><<a href="mailto:mariagoranovic@gmail.com">mariagoranovic@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;"> Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. <br> <br>The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split.<div> <div></div><div class="h5"><br> <br><div class="gmail_quote">On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</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;"> <div><br> On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> <br> maria goranovic wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> I did use -pbc nojump, but that does not help<br> </blockquote> <br> What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact.<br> </blockquote></div> The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if<br> the bilayer is cut half! Or the -pbc mol should be applied ...<div><div></div><div><br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> -Justin<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> The drift is about 1 nm per 10 microseconds .<br> (this is a martini simulation)<br> On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a> <mailto:<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>>> wrote:<br> On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:<br> Hello All (and especially Berk)<br> This is an update of the problem that I was facing earlier. I<br> used to tau_p of 3.0 ps, and the problem does not go away, the<br> bilayers still drifts in the simulation box. So this is<br> probably a bug then?<br> How much is the drift (nm/ns)? Did you use removal of center of mass<br> of the entire system of<br> bilayer/solvent separately?<br> I still cannot understand how to put the bilayer back into the<br> center of the simulation box. As suggested by Justin, I tried to<br> use just one tail atom of a lipid for centering, but that did<br> not work either.<br> I noticed that my bilayer, which is initially at the center of<br> the simulation box, separates into two leaflets at the box edges<br> from the very first step of the simulation itself, but i am not<br> able to correct that using the -center and -boxcenter zero<br> options. Can someone please make a suggestion and help?<br> You have to do use -pbc nojump first and then center ...<br> Thank you so much<br> -Maria<br> -- Maria G.<br> Technical University of Denmark<br> Copenhagen<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br> before posting!<br> Please don't post (un)subscribe requests to the list. 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Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> -- <br> Maria G.<br> Technical University of Denmark<br> Copenhagen<br> ------------------------------------------------------------------------<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote> <br> -- <br> ========================================<br> <br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br> <br> ========================================<br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </blockquote> <br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br></div></div> Please don't post (un)subscribe requests to the list. Use thewww interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<div><div></div><div> <br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br> </div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<br> </div></div></blockquote></div><br><br clear="all"><br>-- <br>Maria G.<br>Technical University of Denmark<br>Copenhagen<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/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/mailing_lists/users.php</blockquote></div><br></div></body></html>