[gmx-users] How to rotate box in editconf

[Mark Abraham]

On Sat, Jun 14, 2014 at 2:06 AM, Rini Gupta <rinisgupta at gmail.com> wrote:

> 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 don't understand what this means, so can't tell what you're trying to
achieve.

Mark

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.
>
> Thanks,
>
> Rini
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