So I got it to center my protein (using -pbc nojump) and keep the trimer and the membrane in tact but it completely destroyed my water. I was hoping I could get the whole simulation box back with the protein in the center. Is that possible?
Thanks, Ilya On Tue, Apr 22, 2008 at 3:25 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote: > Just to clarify. > I would run > > trjconv -f *.gro -s *.tpr -pbc nojump -o out.gro? > > What would I run next? > > Thanks, > > Ilya > > > On Tue, Apr 22, 2008 at 2:59 PM, Xavier Periole <[EMAIL PROTECTED]> wrote: > > > On Tue, 22 Apr 2008 14:14:19 -0700 > > "Ilya Chorny" <[EMAIL PROTECTED]> wrote: > > > > > Hello, > > > > > > I am simulating a trimer in a membrane. In one of my simulation two > > > of the > > > monomers are on one side of the box and the other monomer is on the > > > other > > > side of the box. I tried using trjconv to center the whole thing in > > > the > > > center of my simulation cell but have failed miserably. I also > > > searched > > > around for about an hour and could not find anything. > > > > > > I use trjconv -f *.gro -s *.tpr -center rect -pbc whole -o *.gro. > > > > > first run > > trjconv -pbc nojump > > > > > Any advice? > > > > > > Thanks, > > > > > > Ilya > > > > > > -- > > > Ilya Chorny Ph.D. > > > > > > > ----------------------------------------------------- > > XAvier Periole - PhD > > > > NMR & Molecular Dynamics Group > > University of Groningen > > The Netherlands > > http://md.chem.rug.nl/~periole <http://md.chem.rug.nl/%7Eperiole> > > ----------------------------------------------------- > > _______________________________________________ > > 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 > > > > > > -- > Ilya Chorny Ph.D. > -- Ilya Chorny Ph.D.
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