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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 10 00:19:15 CET 2010

durmaz at 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:


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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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