Hi,
Based on the picture I can think of two possibilities:
1) The system coordinates have been rotated (via e.g. an RMS best-fit)
prior to imaging. The rotation essentially invalidates the unit cell
vectors for those coordinates and the imaging is thus invalid. The solution
is to make sure any rotations occur after imaging. I think this the most
likely.
2) The system density is off for some reason and needs to equilibrate
further via simulation in NPT ensemble.
-Dan
On Wed, May 13, 2020 at 3:46 PM Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Dear amber users,
>
> In the attached link appears the image of the water box after running
> autoimage in cpptraj ambertools20. Why are some waters not imagined back
> to the original box and how can this problem be solved?
>
>
> https://drive.google.com/file/d/1LrQ6QmRvp2xWiLef-f3hJMgzmLI5bPpO/view?usp=sharing
>
> Any insight would be most greatly appreciated.
> Cheers,
> Hector
>
>
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Titular (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
>
>
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Received on Wed May 13 2020 - 15:30:03 PDT
