thanks. things are getting clearer and life's going a little easier, now.
Justin A. Lemkul schrieb: > > > dur...@zib.de wrote: >> hi there, >> >> it's my first steps with gromacs and i can't get rid of the following >> problem: >> >> i set up my box with >> >> editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 >> >> and fill it up with water like >> >> genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p >> complex.top >> >> but when viewing the system of the resulting file (outfile.pdb), >> parts of >> the molecular complex turn out to be outside the box, although the >> box is >> obviously large enough. the complex is not centered, whether i use -c or >> not. i've tried several water models (tip4p, ffamber_tip3p) and all box >> shapes such as an octahedron, dodecah., cube, triclinic. the cubic >> one is >> the only one to result in a properly centered complex. but i prefer >> to use >> other box types. >> >> does anyone have an idea of the stage at which to search the cause for >> that problem? >> >> thanks a lot and regards > > This is just a visualization artifact. See, for instance: > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > You can "correct" it by using trjconv (once you have assembled a .tpr > file): > > trjconv -s *.tpr -f outfile.pdb -pbc mol -ur compact > > -Justin > -- 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
