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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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