[gmx-users] molecule ouside water box

Stefano Meliga smeliga at gmail.com
Wed Aug 26 12:23:40 CEST 2009

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?

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?



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