[gmx-users] How to rotate box in editconf

Rini Gupta rinisgupta at gmail.com
Sat Jun 14 02:06:56 CEST 2014

Dear gmx-users,

Sorry, for asking  such a simple question. But I didn't get any
satisfactory answer searching through mailing lists.

I have prepared a mixed bilayer system containing 300 lipids with box
size 10 10 14 (nm). Visualization confirmed that bilayer is formed in
X-Y plane.
But, in order to see bilayer edge along z-axis, I need to exchange my
x and z coodinates of this bilayer system.
For this, I use editconf utility as:

editconf -f bilayer.gro -rotate -90 -90 -90 -o newbox.gro

However, as expected editconf only rotates molecule coordinates in
desired direction but simulation box remain unchanged.

I tried building a new box using editconf (suggested by some mailing
posts) around it but still my problem is not solved.

editconf -f newbox.gro -box 10 10 14 -o rotate-box.gro

Can anyone please let me know how to shift simulation box around this
shifted system.



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