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 -- 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
