Thanks for the quickly answer. I used 3.3.3 and 3.3.1 version and the lipids of a monocape are above to the other. The lipids are jumping yet after all those changes. I proved each option separately and some combinations of them.
trjconv -s a.tpr -f a.xtc -o b.xtc -center trjconv -s a.tpr -f b.xtc -o c.xtc -pbc whole/res/mol/none trjconv -s a.tpr -f a.xtc -o b.xtc -center -boxcenter tric -pbc none (res/whole....) -boxcenter tric -center and more.. Cheers, Maite On 7/16/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > If you use the new version of Gromacs (3.3.3), there are several options > that > work nicely. Try each of them separately, probably one of them will work, > maybe > a combination will be necessary based on how much your lipids jump around. > > trjconv -center > (choose DPPC for centering) > > trjconv -pbc res > > trjconv -pbc mol > > The last two give somewhat different results, depending on the context, for > reasons I don't yet understand, but usually one of them works :-) > > -Justin > > maite lopez cabezas wrote: >> Hi: >> I equilibrated a DPPC membrane that I built. I want to take a >> snapshot for doing some protein-membrane simulations, but first i have >> to do somethings for eliminating the lipids out of the box. I have >> tried with pbc and fit options like people say in the list and it >> doesn't work. Anybody can help me, please? >> >> I did things like that and more too (with many combinations): >> >> 1) >> trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none >> trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans >> >> 2) >> trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc nojump >> trjconv -s a.tpr -f b.xtc -o c.xtc -pbc whole >> trjconv -s a.tpr -f c.xtc -o d.xtc -fit rot+trans >> >> I'll apreciate any help, >> Maite >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
