<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Nov 5, 2009, at 1:43 PM, maria goranovic wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">I did use -pbc nojump, but that does not help<br></blockquote>It should! you do nojump and then center using the membrane only as a group reference.</div><div>f this does not work translate your trajectory first on the z axis by about one nm. </div><div>It is actually strange that 1 nm derive on the z axis get your bilayer from the </div><div>middle of the box to half out ! This would imply that your box is about two nm </div><div>high! This is smaller than the thickness of a bilayer!<br><blockquote type="cite"><br>The drift is about 1 nm per 10 microseconds .<br></blockquote>this is quite lot<br><blockquote type="cite"><br>(this is a martini simulation)<br></blockquote>This should not make a difference.</div><div>I also noticed that the removal of the COM is not done properly and on </div><div>a long run there are deviations ... smaller than the one you report but </div><div>still. </div><div><br></div><div>how did you remove the COM?<br><blockquote type="cite"><br><div class="gmail_quote">On Thu, Nov 5, 2009 at 1:02 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> On Nov 5, 2009, at 12:09 PM, maria goranovic 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;"> Hello All (and especially Berk)<br> <br> This is an update of the problem that I was facing earlier. I used to tau_p of 3.0 ps, and the problem does not go away, the bilayers still drifts in the simulation box. So this is probably a bug then?<br> </blockquote></div> How much is the drift (nm/ns)? Did you use removal of center of mass of the entire system of<br> bilayer/solvent separately?<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;"> <br> I still cannot understand how to put the bilayer back into the center of the simulation box. As suggested by Justin, I tried to use just one tail atom of a lipid for centering, but that did not work either.<br> <br> I noticed that my bilayer, which is initially at the center of the simulation box, separates into two leaflets at the box edges from the very first step of the simulation itself, but i am not able to correct that using the -center and -boxcenter zero options. Can someone please make a suggestion and help?<br> </blockquote></div> You have to do use -pbc nojump first and then center ...<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> Thank you so much<br> <br> -Maria<br> <br> -- <br> Maria G.<br> Technical University of Denmark<br> Copenhagen<br></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 class="im"> <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> 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 class="h5"> <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>