[Pw_forum] XYZ format

[Giovanni Cantele]

On Oct 10, 2013, at 8:49 PM, Saleem Ayaz <saleemayaz_hu at yahoo.com> wrote:

> Dear users
> When I make structure file for QE calculation I convert cif file to XYZ format and take the atomic positions from there but these atomic positions are not look to be in angstrom. for example some atomic positions of amino acid.  

> The correct atomic positions of first C atom are 0.442, 0.612, 0.803 (Ang) .  

With respect to which reference system? Maybe you should rather check for atomic
distances and angles.



> Can I use these positions?

Yes, if they correspond to the system you would like to study.



>  ATOMIC_POSITIONS {?}
> C 11.861079793 2.966803800 8.127280110
> O 12.509781978 3.985469800 7.796265486
> O 11.516617567 2.651456000 9.302285237
> C 11.377184932 2.032458000 7.026801667
> H 11.452545578 1.096162600 7.340394469
> N 12.229684621 2.211333800 5.820824411
> H 13.094780045 2.076324000 6.097637810
> H 12.186990774 3.124234000 5.410443708
> H 11.963240449 1.545058000 5.294298226
> ...........
> _______________________________________________
> 

By looking to the positions you list using a visualisation software, they do look
reasonable. So maybe they could be just those you want but shifted/rotated.

Giovanni


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