[gmx-users] energy minimization breaks freeze group apart

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 30 01:35:48 CET 2008

> Also, I still have an issue with how Gromacs is building my system. when I
> run
> editconf -f  $protName.gro  -o box.gro -d 1.2 -bt dodecahedron
> Gromacs places the solute in the top corner of the box, rather than
> centering it in the box. Shouldn't it be in the center? What am I doing
> wrong?

Check out editconf -h.  Centering is not default behavior, but you can center
your protein by using editconf -c.


> Thanks!
> Patricia
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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