Hi,
This can happen if you e.g. do imaging after any kind of rotation in
cpptraj (which if you check the output cpptraj should be warning you
not to do). The solution is to image before rotating. I'm actually
working on code now that will fix this issue (i.e. the order won't
matter anymore), but for now make sure you image first.
-Dan
On Mon, Dec 21, 2020 at 5:08 AM Женя Елизарова <zheneliz147.gmail.com> wrote:
>
> Dear Amber developers,
>
> I was trying to remove the rotation of a protein during cpptraj
> post-processing. I used:
> rms :1-327
> but when I looked at the trajectory it seemed like water molecules
> layered on each other. This didn't appear without rms, so I suppose it is
> related to the visualization. Is it possible to post-process files without
> rotation and normal behavior of water molecules?
>
> Best regards,
> Evgenia Elizarova
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Received on Wed Dec 23 2020 - 07:00:02 PST
