[gmx-users] molecule ouside water box

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 26 12:35:06 CEST 2009

Stefano Meliga wrote:
> Hi gmx users,
> I defined an octahedral box with this line:
> $grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6
> and then I solvated my protein with SPC water model:
> $grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs
> I am now watching the trajectory of an MD simulation with a molecular
> visualisation software (VMD) and I noticed 2 unexpected things:
> 1) part of the molecule is outside the box
> 2) the box is cubic
> Although the molecule is out of the box, the periodic boundary
> conditions should ensure a correct behaviour, still, why is it cubic?

Right, because in a periodic system, there is no "outside," nor are there edges.

The cubic appearance of the box is simply a visualization issue.  You can 
retrieve your true box shape by using trjconv -pbc mol -ur compact.


> Note: after solvation, the system was neutralised with genion, then an
> EM steep, an EM cg and a all-bonds constrained MD were performed
> before the actual MD.
> Any ideas?
> Thanks,
> Stefano
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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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