So I got it to work for my trimer by doing the following. 1.) trjconv -f *.xtc -s *.tpr -pbc nojump -o out.xtc 2.) trjconv -f out.xtc -s *.tpr -pbc mol -center -boxcenter rect
The first step unwraps the whole trajectory and the second step wraps it back up. Cheers, Ilya -- Ilya Chorny Ph.D. On Tue, Apr 22, 2008 at 4:30 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > I've often found it necessary to do multiple trjconv steps to get the > result I want. So in this case, I'd probably make sure my protein is > genuinely centered in the box, then take that output .xtc and then make sure > everything is whole and approximately in the box (-pbc whole). > > > ----- Original Message ---- > From: Ilya Chorny <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Tuesday, April 22, 2008 11:52:23 PM > Subject: Re: [gmx-users] How to center my trimer in my simulation box. > > 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 > > > ----------------------------------------------------- > > > _______________________________________________ > > > 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. > > > ------------------------------ > Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it > now.<http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ> > > _______________________________________________ > 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.
_______________________________________________ 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