<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Nov 6, 2009, at 5:32 PM, maria goranovic wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Well, Xavier :). I will give it one more shot, and get back to the list next week !<br></blockquote>I'll be away for a while ... good luck. </div><div><blockquote type="cite"><br><div class="gmail_quote">On Fri, Nov 6, 2009 at 4:45 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">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 class="im"><br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Well .. I mean .. the lipids are not put back into the central simulation cell in the xy plane. so they keep the nojump effect<br> </blockquote></div> Ok, what you describe does not make sense, not that you do not make<br> sense but the fact that the lipids dot not come back to the central cell<br> in the xy plan does not make sense!<br> I really do not see why that could be! Never seen it ...<br> <br> In most cases for membrane proteins the problem of cutting molecules<br> comes from the xy plan not the z direction.<br> <br> If I were you I would check for a last time your tpr file to make sure it is<br> indeed what you think it is and it is fine ... erase all files and redo the<br> all process, something went bad at some point.<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"> <br> what do you mean "expand"? They do not get back in the box meaning they keep the nojump<br> effect or it is just that they have the tail out of the box?<br> -pbc mol will put the COM of the molecule (protein/lipid/water ...) in the box and leave the molecule<br> as a whole (no cutting bonds).<br> <br> <br> Well you can see the bilayer as protein complex where each monomer is<br> a leaflet. Applying -pbc nojump on the trajectory would simply keep the two<br> leaflets together. Then the system can be centered using the bilayer as<br> reference: this would put the bilayer at the center of the z axis. The<br> movements<br> "out of the box" can then be corrected using -pbc mol.<br> It is trivial is the reference structures are correct.<br> <br> I do not think this is the case. In a protein complex, each monomer is bonded to the next amino acid, and therefore -pbc mol works, because the entire protein is a single molecule . In lipids however, why would trjconv treat the leaflet as a monomer?<br> <br> -pbc mol will work on each molecule, see above, but not on the lipid bilayer of course.<br> This is why you use nojump first! and then center ... then the lipid molecules will be put<br> in the box on the xy plan but not across the z axis<br> <br> And -pbc nojump will also work on each molecule, not on a leaflet as a whole.<br> <br> I think the following takes place:<br> <br> The bilayer moves along -z, and some lipids eventually leave the box on one edge, and appear on the other edge. -pbc nojump ensures that the lipids do not do this, and instead continue drifting along -z. thus the center of mass of the lipids should just keep moving along -z after using -pbc nojump. It is therefore easy to correct this drift while using -center.<br> <br> However, the lipids also diffuse in the x and the y direction, but this diffusion is random. THIS TOO, is changed by using -pbc nojump. Thus, pbc nojump changes the center of mass behavior of the lipids in all three directions. It can be corrected for z, because the z-drift is always along one direction (all lipids diffuse either in -z or +z), but cannot be corrected for xy, because individual lipids diffuse randomly (both along +x/y or -x/y)<br> <br></div></div><div class="im"> _______________________________________________<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<br> 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> </div></blockquote><div><div></div><div class="h5"> <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 thewww 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> </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></body></html>