[gmx-users] editconf/genbox: molecular complex outside simulation box

durmaz at zib.de durmaz at zib.de
Tue Mar 9 23:46:42 CET 2010

hi there,

it's my first steps with gromacs and i can't get rid of the following

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

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