I will try centering with one of the lipid tail atoms .. that could solve the problem.
This the way I have specified the comm_groups: nstcomm = 1 comm-grps = Lipid W OR nstcom = 1 comm-grps = system -Maria On Wed, Sep 2, 2009 at 4:04 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > I am not sure how to fix the trajectory that has drifted ... > > But if your bilayer drifts even if you use a removal of the COM for the > water and > bilayer separately that means there is problem in the code! And this should > be > fixed. > > XAvier. > > > On Sep 2, 2009, at 3:36 PM, maria goranovic wrote: > > Dear Experts >> >> I had posted this earlier, but the problem was not solved by earlier >> suggestions. So am posting again. >> >> I am simulating a POPC bilayer using MARTINI. The simulation ran fine, but >> the bilayer drifted towards the edge of the box along the bilayer normal, >> and eventually some of the atoms crossed the box boundaries. In some cases, >> entire lipid molecules crossed the box boundaries. I tried to recenter the >> trajectory, so that the lipid bilayer would be at the center of the box at >> all times. But for some reason, this does not seem to work? I have tried >> simulations using a single comm_group for the entire system, as well as >> separate ones for the lipid and water, but the same problem appears in >> either case. >> >> Typically, for all-atom bilayers, the following set of commands works to >> correct the drift: >> >> #### first convert original trajectory to a temp. xtc ### >> echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center -boxcenter >> zero -pbc mol -n popc.ndx >> #### then convert temp.xtc to the final trajecory ### >> echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center -boxcenter >> zero -pbc mol -n popc.ndx >> >> where groups 3 and 0 are the lipid and the whole system respectively, and >> final.xtc is my final trajectory. >> >> However, this does not work for the MARTINI systems. Looking at the final >> trajectory in VMD, the bilayer is either at the center of the box, or it is >> split at the box edges, with each monomer being in different leaflets. >> >> If I plot the center of mass motion of the entire system in the original >> trajectory .. the system seems to drift by ~ 2-3 angstroms in one direction. >> As a result, water center of mass drifts in the opposite direction (because >> of PBC). >> >> Are there any suggestions to sort this out? One option is to write the >> entire trajectory to .gro files, recenter all of them (depending upon >> whether the bilayer is in the center or is split at the box edge), and >> concatenate the gro files again.but this is tedious, even if scripted. >> >> Please let me know if i can provide any additional info ? >> >> -- >> Maria G. >> Technical University of Denmark >> Copenhagen >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Maria G. Technical University of Denmark Copenhagen
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php