Try e.g. trjconv -pbc mol -trans ? ? ? to have your molecule not span the edges first. You might also need a trjconv -pbc nojump and trjconv -pbc -mol again afterwards before centering. 25 okt 2012 kl. 13.44 skrev Ignacio Fernández Galván:
> I must be doing something wrong, but I can't get trjconv to center the > simulation on a residue. > > The simulation box is cubic, the system is formed by an 8-atom frozen > molecule and 800 water molecules. I try to center the box with: > > $ trjconv -f system.cpt -s system.tpr -o conf.gro -center > > (system.cpt and system.tpr are the result of a simulation) > > I select group "2" (the frozen molecule) as a center group, and I get this in > the output conf.gro: > > 1ACR C1 1 0.074 0.042 1.443 0.0000 0.0000 0.0000 > 1ACR H1 2 0.130 0.139 1.443 0.0000 0.0000 0.0000 > 1ACR O 3 0.133 2.822 1.443 0.0000 0.0000 0.0000 > 1ACR C2 4 2.811 0.056 1.443 0.0000 0.0000 0.0000 > 1ACR H2 5 2.771 0.158 1.443 0.0000 0.0000 0.0000 > 1ACR C3 6 2.731 2.834 1.443 0.0000 0.0000 0.0000 > 1ACR H3a 7 2.622 2.843 1.443 0.0000 0.0000 0.0000 > 1ACR H3b 8 2.775 2.734 1.443 0.0000 0.0000 0.0000 > > as you see, the molecule is clearly broken (a difference of more than 2 nm in > coordinates), and when visualized, it's indeed in the box's edge. > > I've tried with different combinations of -pdb res/mol, -boxcenter > zero/tric/rect, -ur compact, but I always get the molecule broken, sometimes > in a corner, sometimes in an edge. > > In case it matters, the initial configuration for the simulation has: > > 1ACR C1 1 0.138870 0.039109 0.000000 > 1ACR H1 2 0.195321 0.135855 0.000000 > 1ACR O 3 0.197788 -0.067044 0.000000 > 1ACR C2 4 -0.009210 0.052984 0.000000 > 1ACR H2 5 -0.049761 0.154673 0.000000 > 1ACR C3 6 -0.089322 -0.054436 0.000000 > 1ACR H3a 7 -0.198186 -0.045502 0.000000 > 1ACR H3b 8 -0.045500 -0.154639 0.000000 > > and, as I said, this residue (and molecule) is set as frozen, and it is > actually frozen during the simulation. > > Is there some bug/limitation in trjconv? Am I doing something wrong? > > Thanks, > Ignacio > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 [email protected] http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
